AS3MT

arsenite methyltransferase, the group of 7BS small molecule methyltransferases

Basic information

Region (hg38): 10:102869469-102901899

Links

ENSG00000214435 ∙ NCBI:57412 ∙ OMIM:611806 ∙ HGNC:17452 ∙ Uniprot:Q9HBK9 ∙ 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 AS3MT gene.

• Inborn genetic diseases (11 variants)
• not provided (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the AS3MT gene is commonly pathogenic or not.

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.

Variant type	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous						0
missense			11			11
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding					1	1
Total	0	0	11	0	1

Variants in AS3MT

This is a list of pathogenic ClinVar variants found in the AS3MT region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
10-102870074-G-T			Benign (Jul 05, 2018)
10-102872497-A-G		not specified	Uncertain significance (Sep 29, 2022)
10-102872531-G-T		not specified	Uncertain significance (May 17, 2023)
10-102872588-C-G		not specified	Uncertain significance (Oct 03, 2022)
10-102873124-T-C		not specified	Uncertain significance (Aug 04, 2023)
10-102873130-A-G		not specified	Uncertain significance (Oct 27, 2022)
10-102876981-G-A		not specified	Uncertain significance (Aug 30, 2022)
10-102878390-G-A		not specified	Uncertain significance (Aug 16, 2022)
10-102878429-C-A		not specified	Uncertain significance (Feb 06, 2024)
10-102878924-T-C		not specified	Uncertain significance (Oct 12, 2021)
10-102878941-A-G		not specified	Uncertain significance (Mar 21, 2023)
10-102890608-A-G		not specified	Uncertain significance (Mar 20, 2023)
10-102890620-T-C		not specified	Uncertain significance (Dec 21, 2023)
10-102890629-T-C		not specified	Uncertain significance (Nov 22, 2023)
10-102900606-A-G		not specified	Uncertain significance (Dec 28, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
AS3MT	protein_coding	protein_coding	ENST00000369880	11	32384

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
7.98e-11	0.144	124699	0	96	124795	0.000385

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.962	165	204	0.810	0.0000101	2448
Missense in Polyphen		41	53.483	0.76659		689
Synonymous	1.18	59	71.8	0.822	0.00000369	705
Loss of Function	0.529	17	19.5	0.871	8.22e-7	258

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000853	0.000850
Ashkenazi Jewish	0.00	0.00
East Asian	0.000169	0.000167
Finnish	0.00	0.00
European (Non-Finnish)	0.000471	0.000468
Middle Eastern	0.000169	0.000167
South Asian	0.000692	0.000654
Other	0.000353	0.000330

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Catalyzes the transfer of a methyl group from AdoMet to trivalent arsenicals producing methylated and dimethylated arsenicals (PubMed:16407288, PubMed:25997655). It methylates arsenite to form methylarsonate, Me-AsO(3)H(2), which is reduced by methylarsonate reductase to methylarsonite, Me-As(OH)2 (PubMed:16407288, PubMed:25997655). Methylarsonite is also a substrate and it is converted into the much less toxic compound dimethylarsinate (cacodylate), Me(2)As(O)-OH (PubMed:16407288, PubMed:25997655). {ECO:0000269|PubMed:16407288, ECO:0000269|PubMed:25997655}.
• Pathway: Methylation;Phase II - Conjugation of compounds;Biological oxidations;Metabolism;arsenate detoxification I (glutaredoxin) (Consensus)

Recessive Scores

• pRec: 0.126

Intolerance Scores

• loftool: 0.831
• rvis_EVS: 0.55
• rvis_percentile_EVS: 81.38

Haploinsufficiency Scores

• pHI: 0.0906
• hipred: N
• hipred_score: 0.301

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.0702

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium

Mouse Genome Informatics

• Gene name: As3mt
• Phenotype: liver/biliary system phenotype; homeostasis/metabolism phenotype

Gene ontology

• Biological process: toxin metabolic process;arsonoacetate metabolic process;methylation
• Cellular component: cytosol
• Molecular function: arsenite methyltransferase activity;methylarsonite methyltransferase activity