GeneBe

SHMT1

serine hydroxymethyltransferase 1, the group of Serine hydroxymethyltransferase family|MicroRNA protein coding host genes

Basic information

Region (hg38): 17:18327873-18363550

Links

ENSG00000176974 ∙ NCBI:6470 ∙ OMIM:182144 ∙ HGNC:10850 ∙ Uniprot:P34896 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the SHMT1 gene.

  • not_specified (52 variants)
  • not_provided (14 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SHMT1 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000004169.5. Only rare variants are included in the table.

In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.

Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.

EffectPLPVUSLBBSum
synonymous
1
clinvar
3
clinvar
 4
missense
49
clinvar
4
clinvar
2
clinvar
 55
nonsense
0
start loss
1
1
 2
frameshift
0
splice donor/acceptor (+/-2bp)
0
Total 0 0 49 6 6
Loading clinvar variants...

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
SHMT1protein_codingprotein_codingENST00000316694 1135670
pLI Probability
LOF Intolerant 		pRec Probability
LOF Recessive 		Individuals with
no LOFs 		Individuals with
Homozygous LOFs 		Individuals with
Heterozygous LOFs 		Defined p
1.27e-140.02331256560921257480.000366
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense0.3522592750.9400.00001683127
Missense in Polyphen113135.390.834621439
Synonymous-0.6611251161.080.00000744983
Loss of Function0.2052223.10.9540.00000146263

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.001220.00122
Ashkenazi Jewish0.0007990.000794
East Asian0.0005440.000489
Finnish0.0002330.000231
European (Non-Finnish)0.0002210.000220
Middle Eastern0.0005440.000489
South Asian0.0003590.000359
Other0.0004900.000489

dbNSFP

Source: dbNSFP

Function
FUNCTION: Interconversion of serine and glycine (PubMed:8505317, PubMed:24698160). {ECO:0000269|PubMed:24698160, ECO:0000269|PubMed:8505317}.;
Pathway
Antimetabolite Pathway - Folate Cycle, Pharmacodynamics;One carbon pool by folate - Homo sapiens (human);Glycine, serine and threonine metabolism - Homo sapiens (human);Glyoxylate and dicarboxylate metabolism - Homo sapiens (human);Methotrexate Pathway (Cancer Cell), Pharmacodynamics;Thiopurine Pathway, Pharmacokinetics/Pharmacodynamics;S-Adenosylhomocysteine (SAH) Hydrolase Deficiency;Methionine Metabolism;3-Phosphoglycerate dehydrogenase deficiency;Carnitine Synthesis;Methionine Adenosyltransferase Deficiency;Glycine N-methyltransferase Deficiency;Non Ketotic Hyperglycinemia;Glycine and Serine Metabolism;Hypermethioninemia;Methylenetetrahydrofolate Reductase Deficiency (MTHFRD);Homocystinuria-megaloblastic anemia due to defect in cobalamin metabolism, cblG complementation type;sarcosine oncometabolite pathway ;Dimethylglycine Dehydrogenase Deficiency;Hyperglycinemia, non-ketotic;Dimethylglycine Dehydrogenase Deficiency;Sarcosinemia;Cystathionine Beta-Synthase Deficiency;Dihydropyrimidine Dehydrogenase Deficiency (DHPD);Glycine Metabolism;Folate Metabolism;One Carbon Metabolism;Trans-sulfuration and one carbon metabolism;One carbon metabolism and related pathways;Pathways in clear cell renal cell carcinoma;folate polyglutamylation;Folate metabolism;Branched-chain amino acid catabolism;glycine/serine biosynthesis;Metabolism of amino acids and derivatives;Glycine Serine metabolism;Metabolism;Lysine degradation;folate transformations I;glycine betaine degradation;Metabolism of folate and pterines;dTMP <i>de novo</i> biosynthesis (mitochondrial);Metabolism of water-soluble vitamins and cofactors;Metabolism of vitamins and cofactors;superpathway of choline degradation to L-serine;Lysine metabolism;Vitamin B9 (folate) metabolism;Carnitine synthesis;serine and glycine biosynthesis;Validated targets of C-MYC transcriptional activation (Consensus)

Recessive Scores

pRec
0.388

Intolerance Scores

loftool
0.940
rvis_EVS
0.22
rvis_percentile_EVS
68.38

Haploinsufficiency Scores

pHI
0.824
hipred
Y
hipred_score
0.771
ghis
0.419

Essentials

essential_gene_CRISPR
N
essential_gene_CRISPR2
N
essential_gene_gene_trap
N
gene_indispensability_pred
E
gene_indispensability_score
0.821

Gene Damage Prediction

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium

Mouse Genome Informatics

Gene name
Shmt1
Phenotype
neoplasm; liver/biliary system phenotype; homeostasis/metabolism phenotype;

Gene ontology

Biological process
dTMP biosynthetic process;glycine metabolic process;L-serine metabolic process;L-serine catabolic process;one-carbon metabolic process;purine nucleobase biosynthetic process;negative regulation of translation;glycine biosynthetic process from serine;tetrahydrofolate interconversion;carnitine biosynthetic process;tetrahydrofolate metabolic process;folic acid metabolic process;protein tetramerization;protein homotetramerization;cellular response to tetrahydrofolate;cellular response to leukemia inhibitory factor
Cellular component
nucleus;cytosol;extracellular exosome
Molecular function
translation repressor activity, mRNA regulatory element binding;glycine hydroxymethyltransferase activity;protein binding;zinc ion binding;L-allo-threonine aldolase activity;amino acid binding;pyridoxal phosphate binding;identical protein binding;protein homodimerization activity;mRNA 5'-UTR binding;cobalt ion binding;serine binding