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	Gene Summary
	Translation studies in PubMed
	Exon Skipping Events
	Expression
	Expression Regulation
	Associated Genes
	Protein 3D Structure
	Protein-Protein Interaction
	Mutations
	Prognostic Analysis
	Gender Association
	Age Association
	Related Drugs
	Related Diseases

Translation Factor: SHMT2 (NCBI Gene ID:6472)

Gene Summary

Gene Summary

Gene Information	Gene Name: SHMT2
	Gene ID: 6472
	Gene Symbol	SHMT2
	Gene ID	6472
	Gene Name	serine hydroxymethyltransferase 2
	Synonyms	GLYA\|HEL-S-51e\|SHMT
	Cytomap	12q13.3
	Type of Gene	protein-coding
	Description	serine hydroxymethyltransferase, mitochondrialGLY A+epididymis secretory sperm binding protein Li 51eglycine auxotroph A, human complement for hamsterglycine hydroxymethyltransferaseserine aldolaseserine hydroxymethylaseserine hydroxymethyltransfer
	Modification date	20200327
	UniProtAcc	P34897

Child GO biological process term(s) under GO:0006412

GO ID	GO term
GO:0017148	Negative regulation of translation
GO:0006417	Regulation of translation
GO:0032543	Mitochondrial translation
GO:0006412	Translation

Gene ontology of translaction factor with evidence of Inferred from Direct Assay (IDA) from Entrez

Partner	Gene	GO ID	GO term	PubMed ID
Hgene	SHMT2	GO:0006544	glycine metabolic process	25619277\|29180469
Hgene	SHMT2	GO:0006563	L-serine metabolic process	25619277\|29180469
Hgene	SHMT2	GO:0006730	one-carbon metabolic process	11516159\|29180469\|29364879\|29452640
Hgene	SHMT2	GO:0034340	response to type I interferon	24075985
Hgene	SHMT2	GO:0046653	tetrahydrofolate metabolic process	24075985\|25619277
Hgene	SHMT2	GO:0051262	protein tetramerization	25619277
Hgene	SHMT2	GO:0051289	protein homotetramerization	29180469

Inferred gene age of translation factor.

Gene

Inferred gene age group among (0 - 67.6], (67.6 - 355.7], (355.7 - 733], (733 - 1119.25], >1119.25

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Translation Studies in PubMed

We searched PubMed using 'SHMT2[title] AND translation [title] AND human.'

Gene	Title	PMID
SHMT2	Serine Catabolism by SHMT2 Is Required for Proper Mitochondrial Translation Initiation and Maintenance of Formylmethionyl-tRNAs	29452640

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Exon Skipping Events

Skipped exons in TCGA and GTEx based on Ensembl gene isoform structure.
* Click on the image to open the UCSC genome browser with custom track showing this image in a new window.
For more annotations, please visit our ExonSkipDB.

Open reading frame (ORF) analsis of exon skipping events based on Ensembl gene isoform structure.
* Click on the break point to see the gene structure around the break point region using the UCSC Genome Browser.

ENST	Exon skip start (DNA)	Exon Skip end (DNA)	ORF
ENST00000328923	57625263	57625343	Frame-shift
ENST00000328923	57626235	57626358	In-frame
ENST00000328923	57626486	57626626	Frame-shift

Exon skipping position in the amino acid sequence.

ENST	Exon skip start (DNA)	Exon Skip end (DNA)	Len(transcript seq)	Exon skip start (mRNA)	Exon Skip end (mRNA)	Len(amino acid seq)	Exon skip start (AA)	Exon Skip end (AA)
ENST00000328923	57626235	57626358	2554	1047	1169	504	198	239

Potentially (partially) lost protein functional features of UniProt.

UniProtAcc	Exon skip start (AA)	Exon Skip end (AA)	Function feature start (AA)	Function feature end (AA)	Functional feature type	Functional feature desc.
P34897	198	239	30	504	Chain	ID=PRO_0000032562;Note=Serine hydroxymethyltransferase%2C mitochondrial
P34897	198	239	199	208	Alternative sequence	ID=VSP_043088;Note=In isoform 2. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303\|PubMed:15489334;Dbxref=PMID:15489334
P34897	198	239	199	201	Turn	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:6DK3
P34897	198	239	202	204	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:5V7I
P34897	198	239	206	216	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:6DK3
P34897	198	239	219	223	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:6DK3
P34897	198	239	234	244	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:6DK3

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Expression

Gene expression level across TCGA pancancer

Gene expression level across GTEx pantissue

Expression level of gene isoforms across TCGA pancancer

Expression level of gene isoforms across GTEx pantissue

Cancer(tissue) type-specific expression level of Translation factor using z-score distriution

Differential expression between tumor and matched normal (in the cancer types with more than 10 matched samples)

Cancer type	Translation factor	FC	adj.pval
KICH	SHMT2	-1.81014059189576	0.000187873840332031
STAD	SHMT2	-4.23192874050502	0.00114433001726866
CHOL	SHMT2	-3.80594293409998	0.00390625
BRCA	SHMT2	-1.34163093355935	2.71402271977538e-18
LUAD	SHMT2	-2.86545229066375	5.18546916374703e-11

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Expression Regulation

Translation factor expression regulation through miRNA binding

Cancer type

Gene

miRNA

TargetScan binding score (Context++ score percentile)

Coefficient

Pvalue

Translation factor expression regulation through methylation in the promoter of Translation factor

Cancer type	Gene	methyl group b	methyl group a	DEG pval	avg methyl in b	avg methyl in a	avg exp in b	avg exp in a
KIRC	SHMT2	1	2	0.0470912811983256	0.184754385964912	0.244378167937215	-0.553090783963691	-0.366440050572893

Translation factor expression regulation through methylation in the gene body of Translation factor (positive regulation)

Cancer type	Gene	methyl group b	methyl group a	DEG pval	avg methyl in b	avg methyl in a	avg exp in b	avg exp in a
SARC	SHMT2	1	2	0.038432242960311	0.156890972222222	0.298874013605442	-0.479865090388442	-0.278302505354573

Translation factor expression regulation through copy number variation of Translation factor

Cancer type

Gene

Coefficient

Pvalue

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Associated Genes

Strongly correlated genes belong to cellular important gene groups with SHMT2 (coefficient>0.8, pval<0.05, node color based on FC between tumor and matched normal). Significantly associated important genes in the individual cancer types. * Cell metabolism gene: cell metabolism genes from REACTOME (black edge), IUPHAR: drug target genes from IUPHAR (blue edge), Kinase: human kinase genes (brown edge), CGC: cancer gene census genes (orange edge), TSG: tumor suppresor genes (purple edge), Epifactor: epigenetic factors (light blue edge), TF: transcription factors (green)

Cancer type	Gene group	Translation factor	Correlated gene	Coefficient	Pvalue
CHOL	Cell metabolism gene	SHMT2	EBP	0.809173185	1.73E-11
CHOL	Cell metabolism gene	SHMT2	QDPR	0.810685338	1.49E-11
CHOL	Cell metabolism gene	SHMT2	ASL	0.814226202	1.03E-11
CHOL	Cell metabolism gene	SHMT2	ACADS	0.814421074	1.01E-11
CHOL	Cell metabolism gene	SHMT2	MMAB	0.815503132	8.99E-12
CHOL	Cell metabolism gene	SHMT2	GALK1	0.817584182	7.20E-12
TGCT	Cell metabolism gene	SHMT2	TPI1	0.805646048	7.62E-37
TGCT	Cell metabolism gene	SHMT2	CBS	0.813133642	5.05E-38
TGCT	IUPHAR	SHMT2	CBS	0.813133642	5.05E-38
THYM	Cell metabolism gene	SHMT2	DTYMK	0.812695991	6.34E-30
THYM	Cell metabolism gene	SHMT2	RNPS1	0.820103078	7.13E-31
THYM	Cell metabolism gene	SHMT2	POLR3K	0.831047479	2.33E-32
THYM	Cell metabolism gene	SHMT2	TUBA1C	0.836678788	3.65E-33
THYM	Cell metabolism gene	SHMT2	NOP56	0.84417304	2.76E-34
THYM	CGC	SHMT2	CDK4	0.810691054	1.13E-29
THYM	CGC	SHMT2	HMGA1	0.848606406	5.60E-35
THYM	Epifactor	SHMT2	PPM1G	0.807672565	2.64E-29
THYM	Epifactor	SHMT2	HDGF	0.815351159	2.93E-30
THYM	Epifactor	SHMT2	RUVBL1	0.819020591	9.87E-31
THYM	Epifactor	SHMT2	NAP1L4	0.835891697	4.75E-33
THYM	IUPHAR	SHMT2	CDK4	0.810691054	1.13E-29
THYM	IUPHAR	SHMT2	ECE2	0.821989412	4.02E-31
THYM	IUPHAR	SHMT2	MFSD2B	0.848737036	5.34E-35
THYM	Kinase	SHMT2	CDK4	0.810691054	1.13E-29
THYM	TF	SHMT2	HMGA1	0.848606406	5.60E-35
UCS	Cell metabolism gene	SHMT2	DTYMK	0.812695991	6.34E-30
UCS	Cell metabolism gene	SHMT2	RNPS1	0.820103078	7.13E-31
UCS	Cell metabolism gene	SHMT2	POLR3K	0.831047479	2.33E-32
UCS	Cell metabolism gene	SHMT2	TUBA1C	0.836678788	3.65E-33
UCS	Cell metabolism gene	SHMT2	NOP56	0.84417304	2.76E-34
UCS	CGC	SHMT2	CDK4	0.810691054	1.13E-29
UCS	CGC	SHMT2	HMGA1	0.848606406	5.60E-35
UCS	Epifactor	SHMT2	PPM1G	0.807672565	2.64E-29
UCS	Epifactor	SHMT2	HDGF	0.815351159	2.93E-30
UCS	Epifactor	SHMT2	RUVBL1	0.819020591	9.87E-31
UCS	Epifactor	SHMT2	NAP1L4	0.835891697	4.75E-33
UCS	IUPHAR	SHMT2	CDK4	0.810691054	1.13E-29
UCS	IUPHAR	SHMT2	ECE2	0.821989412	4.02E-31
UCS	IUPHAR	SHMT2	MFSD2B	0.848737036	5.34E-35
UCS	Kinase	SHMT2	CDK4	0.810691054	1.13E-29
UCS	TF	SHMT2	HMGA1	0.848606406	5.60E-35

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Protein structure

Protein 3D structure
Visit iCn3D.

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Protein-Protein Interaction

Protein-protein interaction networks
* Overlap between up-regulated DEGs (log2FC<-1 and adj.P<0.05) and STRING PPI network (center: Translation factor, node: DEGs, edges: weighted by -log2(adj.P))

Overlap between down-regulated DEGs (log2FC>1 and adj.P<0.05) and STRING PPI network (center: Translation factor, node: DEGs, edges: weighted by -log2(adj.P))

* Edge colors based on TCGA cancer types.

* Overlap between DEGs (log2FC>1 and adj.P<0.05) and STRING PPI network per cancer (center: Translation factor, node: DEGs, node color: log2FC, edges: weighted by -log2(adj.P))

Cancer type	Translation factor	Interacting protein coding gene	FC	adj.pval
KICH	SHMT2	ATIC	1.09331845723325	0.000120222568511963
PRAD	SHMT2	BRCC3	1.14424201416962	0.000128425549333124
LIHC	SHMT2	BRE	-6.61176219859594	0.000131999218450268
LUAD	SHMT2	BRE	-3.36660283460559	0.000178750801498778
KIRC	SHMT2	FAM175B	-1.30808319274535	0.000205518118020117
KIRC	SHMT2	MTHFD1	-1.93638174369857	0.00050811011383314
KICH	SHMT2	GART	1.11145587028427	0.000808119773864746
ESCA	SHMT2	ATIC	-3.8726581413577	0.0009765625
KICH	SHMT2	MTHFD2	-1.12323973381203	0.00102710723876953
KICH	SHMT2	MTHFD1L	-1.41915280490481	0.00129634141921997
CHOL	SHMT2	AMT	-1.94107060302683	0.00390625
CHOL	SHMT2	MTHFD1L	-4.06499253361442	0.00390625
CHOL	SHMT2	MTHFD2	-1.43112243218151	0.00390625
ESCA	SHMT2	MTHFD1	-3.26939074305335	0.009765625
HNSC	SHMT2	BRCC3	-1.8413518216242	0.0160082414213321
BRCA	SHMT2	MTHFD1	-7.96417208719303	0.0176938185073105
LUSC	SHMT2	BRE	-1.75174851461608	0.0188718129321701
HNSC	SHMT2	FAM175B	-1.25207949623851	0.0217607007634797
CHOL	SHMT2	BRCC3	-3.81857882200804	0.02734375
PRAD	SHMT2	AMT	-2.59259541641874	1.02073776774091e-07
THCA	SHMT2	ATIC	-3.26391781299857	1.38467683131598e-09
KIRC	SHMT2	MTHFD1L	-1.69917415940831	1.67130433779115e-06
LUAD	SHMT2	MTHFD1	-2.15031372279412	2.1660933617938e-09
BRCA	SHMT2	BRCC3	1.98488824435185	2.21265219234548e-20
HNSC	SHMT2	ATIC	-3.95366159660393	2.41986685978191e-06
LIHC	SHMT2	MTHFD1L	-1.09891649768116	3.74721971423485e-08
PRAD	SHMT2	MTHFD2	-5.91588409449604	3.88449147505731e-08
KIRC	SHMT2	MTHFD2	-1.02667254420535	4.37068172976619e-11
HNSC	SHMT2	GART	2.02331952914874	7.62444699375921e-05
KIRP	SHMT2	AMT	-2.50521939646022	8.09784978628159e-07
STAD	SHMT2	MTHFD1	-4.08327414989158	8.09784978628159e-07
COAD	SHMT2	AMT	-3.86525397362641	8.94069671630861e-08
KIRC	SHMT2	AMT	-1.96757728414223	9.27353127921009e-13

Protein-protein interactors with this translation factor (BIOGRID-3.4.160)

PPI interactors with SHMT2

EIF1B, GNAS, BRCC3, BRE, BABAM1, DDA1, UBA5, ICT1, PPARD, HDAC5, NDRG1, CUL3, CUL1, APP, ATF2, ADRB2, APEH, CAND1, CTTN, GSPT2, IDE, NASP, ARFIP1, ATG7, ATP6V1C1, CUL5, CYHR1, H1FX, HIST1H1B, IVNS1ABP, JMJD6, LUC7L2, PAWR, PSMG3, SEC24D, SHMT1, SNX1, STAT1, TBC1D15, VPS35, SNX6, HUWE1, ARL6IP1, CMTM5, NOC2L, HES4, MTOR, UBR4, HP1BP3, E2F2, RSRP1, ARID1A, MAP3K6, RCC1, ZBTB8OS, YARS, KIAA0754, BMP8B, SZT2, LRRC42, MRPL37, DNAJB4, CCBL2, SNORD21, SNORA66, FNBP1L, PALMD, STRIP1, NOTCH2NL, MRPS21, GOLPH3L, PRUNE, S100A11, TPM3, KIAA0907, LMNA, MEF2D, COPA, NDUFS2, SNORD76, RABGAP1L, SCARNA3, C1orf21, LIN9, PARP1, AHCTF1, FAM110C, PTRHD1, GPATCH11, LRPPRC, CAMKMT, EFEMP1, MEIS1, POLR1A, COX5B, PDCL3, NPAS2, BIN1, IWS1, NAB1, FAM117B, ABI2, COL4A3, SCARNA5, HJURP, ATG4B, ZNF860, SNORA6, RBM6, ARHGEF3, THOC7, CCDC58, ISY1, MBD4, RYK, MRPS22, ACTL6A, ABCC5, SNORA63, XXYLT1, DGKQ, EVC, GRPEL1, HSP90AB2P, MED28, OCIAD1, SEC31A, MRPS18C, WDFY3, HERC3, FAT4, HMGB2, NR2F1-AS1, SNORA13, TNFAIP8, RAPGEF6, HSPA4, HSPA9, SNORA74A, HARS2, FBXO38, STK10, SNORA74B, UIMC1, GRK6, PDLIM7, DDX41, HNRNPAB, EXOC2, BPHL, FARS2, SCARNA27, TBC1D7, RNF144B, HIST1H4E, HIST1H2AE, HIST1H4I, HIST1H2BO, PBX2, ZNF76, NFYA, MRPS10, TRERF1, TTK, SNX14, ZUFSP, SNORA33, IFNGR1, HEBP2, FBXO5, SCAF8, TFB1M, WDR27, SNX8, NOD1, SNORA5A, CRCP, GATAD1, SAMD9, PTCD1, ATP5J2-PTCD1, TRIP6, PMPCB, PSMC2, LOC407835, COPG2, NUP205, LOC155060, ABCF2, DMTN, BIN3, GTF2E2, SNORD54, MTFR1, STAU2, GDAP1, RIPK2, DECR1, PLEKHF2, YWHAZ, UTP23, ZNF623, SCRIB, KANK1, KIAA0020, KDM4C, MPDZ, ACO1, NFX1, UBAP1, TLN1, CREB3, HINT2, C9orf40, NOL8, NANS, CCP110, TTLL11, HSPA5, CCBL1, FNBP1, SNORD24, SNORA43, SNORA17, DPH7, USP6NL, KIAA1217, CUL2, BMS1, HERC4, DNA2, AGAP11, ALDH18A1, GOT1, C10orf76, BBIP1, SNORA52, SNORA54, DNHD1, ILK, ZNF215, SNORA45B, COPB1, ELP4, MADD, PSMC3, NDUFS3, CPSF7, FEN1, SNORD22, SSH3, RELT, SNORA8, ANKRD49, AMOTL1, ENDOD1, IL18, CEP164, VPS11, HINFP, FOXRED1, CPNE8, KIF21A, PPHLN1, HDAC7, LIMA1, RAB5B, SMARCC2, CS, SPRYD4, INHBE, RASSF9, NTN4, APAF1, MIR3652, PXN, RNF10, USPL1, INTS6, PIBF1, RAP2A, FKSG29, TUBGCP3, PCID2, SNORD9, MLH3, FLVCR2, GTF2A1, DDX24, BTBD6, WHAMMP2, AQR, KNSTRN, CHP1, ADAL, TP53BP1, PIN4P1, GABPB1-AS1, TMOD2, TCF12, GCOM1, MYO1E, HMG20A, RHBDF1, CLUAP1, SPN, SNORA30, C16orf93, RPGRIP1L, ARL2BP, NUTF2, EDC4, NFATC3, PDPR, DHX38, OSGIN1, KLHDC4, PRPF8, WDR81, CHD3, PFAS, POLDIP2, ALDOC, MYO18A, COPRS, ZNF207, SNORD7, SNORA21, RAPGEFL1, NT5C3B, STAT3, AOC2, DHX8, HEXIM1, LUC7L3, SRSF1, MKS1, METTL2A, STRADA, SNORD104, PLEKHM1P, SAP30BP, EXOC7, SCARNA16, TBC1D16, HGS, NDC80, FAM210A, TTC39C, ELP2, MBD1, PIGN, ADNP2, WDR18, GIPC3, HNRNPM, TYK2, SNORD41, RNASEH2A, AKAP8L, RAB8A, UNC13A, CRLF1, COPE, RFXANK, ZNF792, SUPT5H, ATP1A3, CADM4, PPP5C, STRN4, PRMT1, ZNF419, ZNF544, ZNF8, A1BG, NOP56, ITPA, XRN2, RALY, CEP250, ZNFX1, GMEB2, BACH1, CRYZL1, NDUFV3, NIPSNAP1, TAB1, ATF4, XRCC6, CA5B, POLA1, RBM10, EBP, HDAC6, SPIN4, PIN4, MORC4, GLUD2, ENOX2, MBNL3, DKC1, FUNDC2, CUL7, OBSL1, ESR1, ILF2, FBXW11, DCTN2, DDX1, EIF4EBP1, HSPE1, MAPK12, NAPRT, SCLY, ATP6V1A, EZR, GORASP2, NLRP13, PAFAH1B2, PPP1R8, PRRC1, RHOA, YWHAE, NTRK1, CTR9, Nfyc, Itsn2, Ruvbl1, Tnpo1, U2AF2, PPM1G, FAM175B, TMEM184A, DYNLL2, DYNLL1, DLD, PDHA1, SDHA, SOAT1, IFNAR1, FBXO7, PTPN23, BMPR1A, PPP6C, YAF2, EFTUD2, CCDC155, CLEC2D, MAL2, RIOK1, AGR2, MYC, AIFM1, MRM1, HSPD1, PDK1, COX14, SFXN1, TRMT61B, AURKAIP1, METTL14, KIAA1429, PHB, NR2C2, UCHL3, CTCF, DYNC1LI2, DCTN4, SND1, HADHA, AASS, P4HA1, HSP90AA1, CLPP, LDHB, HSP90AB1, ATP5C1, GAP43, OAT, VDAC2, ATP5F1, ACOT9, VCP, CTNNB1, NENF, ME2, BCAP31, HK1, CCT3, CCT7, NNT, SQSTM1, SYNJ2BP, TXNRD1, BCL2L14, NT5C3A, DUSP21, DUSP28, BIRC3, SHMT2, TRIM28, CAB39, PLEKHA4, ZC3H18, PEBP1, PRKCE, KIAA0895, PARL, E, nsp9, ORF6, IMMP2L, GRSF1, DUX4, ANLN, CHMP4C, ECT2, KIF14, KIF20A, KIF23, ARHGAP36, DOCK8, ARHGAP27, ARHGEF16, ARHGAP39, ARHGEF15, MYO9A, Ophn1, PREX1, Stard13, ACAD9, AUH, C12orf65, C17orf80, C1QBP, C21orf33, C6orf203, C8orf82, MCUR1, CCDC90B, CHCHD1, COX15, CRYZ, DDX28, DHX30, FASTKD2, FASTKD3, FASTKD5, GFM1, GFM2, LONP1, MCU, CCDC109B, MDH2, METTL15, METTL17, MRPL11, MRPS12, MRPS26, MRRF, MTERF3, MTFMT, MTG2, MTIF2, MTIF3, MTRF1, MTRF1L, NGRN, OTC, PMPCA, RMND1, RPUSD3, RPUSD4, SLC25A12, SLIRP, SSBP1, SURF1, TACO1, TBRG4, TEFM, TFAM, C19orf52, TMEM70, TRUB2, TSFM, TUFM, VWA8, EXD2, ACACA, NDN, HULC, ILF3, RBM39, WDR76, DNAJA3, DNAJC15, DNAJC19, DNAJC28, DNAJC30, DNAJC4, HSCB, SF3A1, SF3A3, CANX, IDH2, ERP44, GGH, AHCY, ACTN4, SMCHD1, ACO2, TRIM21, DDX58, OGT, CD274, AARS2, COX4I1, COX8A, TRAP1, NAA40, BGLT3, DPP9, DPP8, RPS4Y1, SPRTN, N, nsp11, nsp14, nsp15, CCNF, SLFN11,

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Mutations

Clinically associated variants from ClinVar.

Gene	Chr	Position	RefSeq	VarSeq	RefSeeq	VarType	Pathogenic	Disease	VarInfo
SHMT2	chr12	57623363	A	G	single_nucleotide_variant	Benign	not_provided
SHMT2	chr12	57623519	G	A	single_nucleotide_variant	Benign	not_provided	SO:0001619\|non-coding_transcript_variant,SO:0001623\|5_prime_UTR_variant	SO:0001619\|non-coding_transcript_variant,SO:0001623\|5_prime_UTR_variant
SHMT2	chr12	57624701	C	T	single_nucleotide_variant	Benign	not_provided	SO:0001583\|missense_variant,SO:0001619\|non-coding_transcript_variant	SO:0001583\|missense_variant,SO:0001619\|non-coding_transcript_variant
SHMT2	chr12	57625490	C	T	single_nucleotide_variant	Benign	not_provided	SO:0001627\|intron_variant	SO:0001627\|intron_variant
SHMT2	chr12	57625653	C	T	single_nucleotide_variant	Pathogenic	Neurodevelopmental_disorder_with_cardiomyopathy,_spasticity,_and_brain_abnormalities	SO:0001583\|missense_variant,SO:0001619\|non-coding_transcript_variant	SO:0001583\|missense_variant,SO:0001619\|non-coding_transcript_variant
SHMT2	chr12	57625950	G	A	single_nucleotide_variant	Benign	not_provided	SO:0001627\|intron_variant	SO:0001627\|intron_variant
SHMT2	chr12	57626018	C	T	single_nucleotide_variant	Benign	not_provided	SO:0001619\|non-coding_transcript_variant,SO:0001819\|synonymous_variant	SO:0001619\|non-coding_transcript_variant,SO:0001819\|synonymous_variant
SHMT2	chr12	57626038	C	G	single_nucleotide_variant	Likely_pathogenic	Neurodevelopmental_disorder_with_cardiomyopathy,_spasticity,_and_brain_abnormalities\|Neurodevelopmental_disorder	SO:0001583\|missense_variant,SO:0001619\|non-coding_transcript_variant	SO:0001583\|missense_variant,SO:0001619\|non-coding_transcript_variant
SHMT2	chr12	57627074	G	T	single_nucleotide_variant	Benign	not_provided	SO:0001619\|non-coding_transcript_variant,SO:0001819\|synonymous_variant	SO:0001619\|non-coding_transcript_variant,SO:0001819\|synonymous_variant
SHMT2	chr12	57627528	TTAGGTG	A	Indel	Pathogenic	Neurodevelopmental_disorder_with_cardiomyopathy,_spasticity,_and_brain_abnormalities	SO:0001574\|splice_acceptor_variant	SO:0001574\|splice_acceptor_variant
SHMT2	chr12	57627541	A	G	single_nucleotide_variant	Likely_pathogenic	Neurodevelopmental_disorder_with_cardiomyopathy,_spasticity,_and_brain_abnormalities	SO:0001583\|missense_variant,SO:0001619\|non-coding_transcript_variant	SO:0001583\|missense_variant,SO:0001619\|non-coding_transcript_variant
SHMT2	chr12	57627543	A	G	single_nucleotide_variant	Likely_pathogenic	Neurodevelopmental_disorder_with_cardiomyopathy,_spasticity,_and_brain_abnormalities\|Neurodevelopmental_disorder	SO:0001583\|missense_variant,SO:0001619\|non-coding_transcript_variant	SO:0001583\|missense_variant,SO:0001619\|non-coding_transcript_variant
SHMT2	chr12	57627591	C	T	single_nucleotide_variant	Uncertain_significance	not_provided	SO:0001583\|missense_variant,SO:0001619\|non-coding_transcript_variant	SO:0001583\|missense_variant,SO:0001619\|non-coding_transcript_variant
SHMT2	chr12	57627675	G	A	single_nucleotide_variant	Pathogenic	Neurodevelopmental_disorder_with_cardiomyopathy,_spasticity,_and_brain_abnormalities	SO:0001583\|missense_variant,SO:0001619\|non-coding_transcript_variant	SO:0001583\|missense_variant,SO:0001619\|non-coding_transcript_variant
SHMT2	chr12	57627717	G	A	single_nucleotide_variant	Benign	not_provided	SO:0001627\|intron_variant	SO:0001627\|intron_variant
SHMT2	chr12	57627810	A	C	single_nucleotide_variant	Pathogenic	Neurodevelopmental_disorder_with_cardiomyopathy,_spasticity,_and_brain_abnormalities	SO:0001583\|missense_variant,SO:0001619\|non-coding_transcript_variant	SO:0001583\|missense_variant,SO:0001619\|non-coding_transcript_variant
SHMT2	chr12	57628124	C	G	single_nucleotide_variant	Pathogenic	Neurodevelopmental_disorder_with_cardiomyopathy,_spasticity,_and_brain_abnormalities	SO:0001583\|missense_variant,SO:0001619\|non-coding_transcript_variant	SO:0001583\|missense_variant,SO:0001619\|non-coding_transcript_variant

nsSNVs with sample frequency (size of circle) from TCGA 33 cancers.

SNVs and Indels

Gene	Cancer type	Chromosome	Start	End	RefSeeq	MutSeq	Mutation type	AAchange	# samples
SHMT2	KIRC	chr12	57627609	57627609	G	A	Missense_Mutation	p.E401K	5
SHMT2	STAD	chr12	57627675	57627675	G	A	Missense_Mutation	p.G423S	4
SHMT2	STAD	chr12	57627077	57627077	G	-	Frame_Shift_Del	p.Q324fs	4
SHMT2	PAAD	chr12	57626282	57626282	G	A	Missense_Mutation	p.R214Q	3
SHMT2	LIHC	chr12	57627083	57627083	C	-	Frame_Shift_Del	p.G326fs	3
SHMT2	STAD	chr12	57626616	57626616	C	T	Nonsense_Mutation	p.R283*	3
SHMT2	PRAD	chr12	57626237	57626237	C	T	Missense_Mutation	p.P103L	3
SHMT2	ESCA	chr12	57627884	57627884	A	G	Missense_Mutation	p.S460G	3
SHMT2	PAAD	chr12	57625629	57625629	G	A	Missense_Mutation	p.A149T	2
SHMT2	STAD	chr12	57626343	57626343	C	T	Silent	p.Y234Y	2
SHMT2	ESCA	chr12	57627050	57627050	C	A	Silent	p.I315I	2
SHMT2	UCEC	chr12	57628070	57628070	C	T	Missense_Mutation	p.R481C	2
SHMT2	ESCA	chr12	57626051	57626051	C	T	Silent	p.F190F	2
SHMT2	STAD	chr12	57627016	57627016	G	A	Missense_Mutation		2
SHMT2	STAD	chr12	57626584	57626584	A	G	Missense_Mutation		2
SHMT2	KIRC	chr12	57626066	57626066	T	-	Frame_Shift_Del	p.Y195fs	2
SHMT2	LIHC	chr12	57626600	57626600	T	C	Silent		2
SHMT2	STAD	chr12	57627016	57627016	G	A	Missense_Mutation	p.G304D	2
SHMT2	KIRP	chr12	57624649	57624649	C	G	Missense_Mutation	p.Q33E	2
SHMT2	STAD	chr12	57626584	57626584	A	G	Missense_Mutation	p.D272G	2
SHMT2	KIRP	chr12	57625677	57625677	G	C	Missense_Mutation	p.D165H	2
SHMT2	LIHC	chr12	57625269	57625269	C	A	Missense_Mutation		2
SHMT2	STAD	chr12	57627591	57627591	C	T	Missense_Mutation	p.R395W	2
SHMT2	PAAD	chr12	57626282	57626282	G	A	Missense_Mutation		2
SHMT2	BRCA	chr12	57626352	57626352	G	A	Missense_Mutation	p.M237I	2
SHMT2	HNSC	chr12	57626334	57626334	C	G	Silent	p.L231L	2
SHMT2	PAAD	chr12	57626358	57626358	G	T	Missense_Mutation		2
SHMT2	STAD	chr12	57628071	57628071	G	A	Missense_Mutation	p.R481H	2
SHMT2	CESC	chr12	57628084	57628084	C	G	Silent		2
SHMT2	LIHC	chr12	57625269	57625269	C	A	Missense_Mutation	p.F79L	2
SHMT2	SARC	chr12	57627611	57627611	G	T	Missense_Mutation		2
SHMT2	UCEC	chr12	57624596	57624596	G	T	Missense_Mutation	p.R15I	2
SHMT2	HNSC	chr12	57627425	57627425	G	A	Missense_Mutation	p.R368Q	2
SHMT2	CESC	chr12	57625512	57625512	G	C	Missense_Mutation		2
SHMT2	KIRP	chr12	57627365	57627365	G	T	Missense_Mutation		2
SHMT2	ESCA	chr12	57627884	57627884	A	G	Missense_Mutation		2
SHMT2	UCEC	chr12	57625551	57625551	G	A	Missense_Mutation	p.A123T	2
SHMT2	PAAD	chr12	57626358	57626358	G	T	Missense_Mutation	p.E239D	2
SHMT2	ESCA	chr12	57627050	57627050	C	A	Silent		2
SHMT2	UCEC	chr12	57627877	57627877	G	A	Silent	p.E457	2
SHMT2	HNSC	chr12	57626045	57626045	C	G	Missense_Mutation	p.I188M	2
SHMT2	CESC	chr12	57628084	57628084	C	G	Silent	p.L485	1
SHMT2	KIRP	chr12	57624649	57624649	C	G	Missense_Mutation		1
SHMT2	LIHC	chr12	57626285	57626285	T	-	Frame_Shift_Del	p.L215fs	1
SHMT2	SARC	chr12	57627569	57627569	G	T	Silent		1
SHMT2	STAD	chr12	57626018	57626018	C	T	Missense_Mutation		1
SHMT2	BLCA	chr12	57625341	57625341	G	A	Silent		1
SHMT2	HNSC	chr12	57626532	57626533	-	T	Frame_Shift_Ins	p.Q255fs	1
SHMT2	COAD	chr12	57625291	57625291	G	A	Missense_Mutation	p.A66T	1
SHMT2	LGG	chr12	57627032	57627032	C	T	Silent	p.Y309Y	1
SHMT2	SKCM	chr12	57627814	57627814	C	T	Silent	p.F415F	1
SHMT2	BLCA	chr12	57627603	57627603	G	A	Missense_Mutation		1
SHMT2	COAD	chr12	57626546	57626546	G	T	Silent	p.V238V	1
SHMT2	LGG	chr12	57627032	57627032	C	T	Nonsense_Mutation		1
SHMT2	PAAD	chr12	57625629	57625629	G	A	Nonsense_Mutation	p.W43*	1
SHMT2	STAD	chr12	57625344	57625344	G	A	Splice_Site	.	1
SHMT2	HNSC	chr12	57626045	57626045	C	G	Missense_Mutation		1
SHMT2	LUAD	chr12	57627019	57627019	G	T	Missense_Mutation	p.R305L	1
SHMT2	SKCM	chr12	57627354	57627354	C	T	Silent	p.T323T	1
SHMT2	BLCA	chr12	57626564	57626564	C	T	Silent	p.P265P	1
SHMT2	COAD	chr12	57626582	57626582	G	A	Silent	p.A250A	1
SHMT2	PAAD	chr12	57626358	57626358	G	T	Splice_Site	p.E239_splice	1
SHMT2	STAD	chr12	57625344	57625344	G	A	Splice_Site	p.R104_splice	1
SHMT2	SKCM	chr12	57626290	57626290	C	T	Missense_Mutation	p.R196W	1
SHMT2	HNSC	chr12	57626558	57626558	G	A	Silent		1
SHMT2	LUAD	chr12	57626980	57626980	A	T	Missense_Mutation	p.Y292F	1
SHMT2	BLCA	chr12	57625341	57625341	G	A	Silent	p.K103K	1
SHMT2	COAD	chr12	57627815	57627815	C	T	Missense_Mutation	p.R416C	1
SHMT2	LIHC	chr12	57627867	57627867	T	C	Missense_Mutation		1
SHMT2	PAAD	chr12	57625629	57625629	G	A	Missense_Mutation		1
SHMT2	STAD	chr12	57628067	57628067	C	T	Nonsense_Mutation	p.Q480*	1
SHMT2	SKCM	chr12	57626237	57626237	C	T	Missense_Mutation	p.P178L	1
SHMT2	HNSC	chr12	57626334	57626334	C	G	Silent		1
SHMT2	LUSC	chr12	57626301	57626301	C	G	Silent	p.L220L	1
SHMT2	BLCA	chr12	57627603	57627603	G	A	Missense_Mutation	p.V399M	1
SHMT2	DLBC	chr12	57624701	57624701	C	T	Missense_Mutation	p.S50L	1
SHMT2	PRAD	chr12	57626237	57626237	C	T	Missense_Mutation	p.P199L	1
SHMT2	SKCM	chr12	57628078	57628078	C	T	Silent	p.A462A	1
SHMT2	HNSC	chr12	57627425	57627425	G	A	Missense_Mutation		1
SHMT2	MESO	chr12	57627365	57627365	G	T	Missense_Mutation	p.R348L	1
SHMT2	BLCA	chr12	57624779	57624779	C	G	Nonsense_Mutation	p.S76*	1
SHMT2	KIRP	chr12	57625342	57625342	A	G	Missense_Mutation	p.R104G	1
SHMT2	ESCA	chr12	57627083	57627083	C	-	Frame_Shift_Del	p.H328fs	1
SHMT2	LIHC	chr12	57627867	57627867	T	C	Missense_Mutation	p.I454T	1
SHMT2	THYM	chr12	57625504	57625504	G	T	Missense_Mutation	p.G107V	1
SHMT2	SKCM	chr12	57627814	57627814	C	T	Silent	p.F436F	1
SHMT2	HNSC	chr12	57626532	57626533	-	-	Frame_Shift_Ins		1
SHMT2	OV	chr12	57627397	57627397	C	T	Missense_Mutation	p.R359W	1
SHMT2	KIRP	chr12	57625677	57625677	G	C	Missense_Mutation	p.D144H	1
SHMT2	LIHC	chr12	57627373	57627373	T	C	Missense_Mutation	p.S351P	1
SHMT2	SARC	chr12	57624685	57624685	G	T	Missense_Mutation		1
SHMT2	THYM	chr12	57627039	57627039	G	T	Nonsense_Mutation		1
SHMT2	SKCM	chr12	57627354	57627354	C	T	Silent	p.T344T	1
SHMT2	KIRP	chr12	57624649	57624649	C	G	Missense_Mutation	p.Q12E	1
SHMT2	ESCA	chr12	57626051	57626051	C	T	Missense_Mutation	p.S85L	1
SHMT2	SKCM	chr12	57626290	57626290	C	T	Missense_Mutation	p.R217W	1
SHMT2	PAAD	chr12	57626329	57626329	C	A	Missense_Mutation		1
SHMT2	STAD	chr12	57626616	57626616	C	T	Nonsense_Mutation	p.R283X	1
SHMT2	LIHC	chr12	57627403	57627403	A	G	Missense_Mutation	p.M361V	1
SHMT2	SARC	chr12	57628071	57628071	G	A	Missense_Mutation		1
SHMT2	SKCM	chr12	57628077	57628077	C	T	Missense_Mutation	p.A483V	1
SHMT2	BLCA	chr12	57626564	57626564	C	T	Silent		1
SHMT2	HNSC	chr12	57626558	57626558	G	A	Silent	p.V263V	1
SHMT2	STAD	chr12	57626068	57626068	A	G	Missense_Mutation	p.K196R	1
SHMT2	CESC	chr12	57625512	57625512	G	C	Missense_Mutation	p.E110Q	1
SHMT2	KIRP	chr12	57625677	57625677	G	C	Missense_Mutation		1
SHMT2	LIHC	chr12	57627026	57627026	C	-	Frame_Shift_Del	p.I307fs	1
SHMT2	SARC	chr12	57626538	57626538	G	A	Missense_Mutation	p.G257S	1
SHMT2	SKCM	chr12	57628078	57628078	C	T	Silent	p.A483A	1
SHMT2	BLCA	chr12	57626582	57626582	G	A	Silent		1

Copy number variation (CNV) of SHMT2
* Click on the image to open the original image in a new window.

Fusion gene breakpoints (product of the structural variants (SVs)) across SHMT2
* Click on the image to open the UCSC genome browser with custom track showing this image in a new window.

Fusion genes with this translation factor from FusionGDB2.0.

FusionGDB2 ID	Disease	Sample	Hgene	Hchr	Hbp	Hstrand	Tgene	Tchr	Tbp	Tstrand
44896	N/A	EC535118	ASNA1	chr19	12858892	+	SHMT2	chr12	57628029	-
44896	N/A	BM150797	CCDC102B	chr18	66541722	+	SHMT2	chr12	57628508	-
44896	SKCM	TCGA-GN-A26D-06A	CNOT2	chr12	70637260	+	SHMT2	chr12	57624586	+
44896	N/A	BC009320	COX8A	chr11	63742141	-	SHMT2	chr12	57626576	+
44897	N/A	BM150812	LINC00466	chr1	63661402	-	SHMT2	chr12	57628509	-
96280	N/A	BF526018	SHMT2	chr12	57628509	+	DISC1FP1	chr11	90199445	+
93285	N/A	AV698095	SHMT2	chr12	57628509	+	EBAG9	chr8	110574147	-
81730	KIRC	TCGA-CZ-5465-01A	SHMT2	chr12	57624783	+	NDUFA4L2	chr12	57629592	-
81730	N/A	BG236790	SHMT2	chr12	57628729	+	NDUFA4L2	chr12	57628731	+
99248	SKCM	TCGA-GN-A26D-06A	SHMT2	chr12	57627893	+	SLC16A7	chr12	60154906	+
99248	SKCM	TCGA-GN-A26D-06A	SHMT2	chr12	57627893	+	SLC16A7	chr12	60165000	+
81730	GBM	TCGA-28-5207-01A	SHMT2	chr12	57627893	+	SLC26A10	chr12	58018649	+
88433	N/A	BG034541	SHMT2	chr12	57628457	+	SYNE2	chr14	64617561	+
98732	N/A	CA489801	SHMT2	chr12	57628328	+	TMEM222	chr1	27653032	-

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Prognostic Analysis

Kaplan-Meier plots with logrank tests of overall survival (OS)

Cancer type

Translation factor

Coefficent

Hazard ratio

Wald test pval

Likelihool ratio pval

Logrank test pval

# samples

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Translation factor and Gender

Differential gene expression between female and male. (Wilcoxon test, pval<0.05)

Cancer type	Translation factor	pval	adj.p
HNSC	SHMT2	0.00681350927401096	0.19

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Translation factor and Age

Differential gene expression between young and old age groups (Wilcoxon test, pval<0.05)

Cancer type	Translation factor	pval	adj.p
LIHC	SHMT2	5.30971370269198e-06	0.00018
BRCA	SHMT2	0.00975349346426652	0.31
ESCA	SHMT2	0.0159792694854436	0.5
BLCA	SHMT2	0.0171389355582837	0.51
THYM	SHMT2	0.0383557436267372	1

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Related Drugs

Drugs targeting genes involved in this translation factor.
(DrugBank Version 5.1.8 2021-05-08)

UniProtAcc

DrugBank ID

Drug name

Drug activity

Drug type

Drug status

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Related Diseases

Diseases associated with this translation factor.
(DisGeNet 4.0)

Disease ID	Disease Name	# PubMeds	Disease source
C0007131	Non-Small Cell Lung Carcinoma	1	CTD_human