ARMT1

acidic residue methyltransferase 1

Basic information

Region (hg38): 6:151452258-151470101

Previous symbols: [ "C6orf211" ]

Links

ENSG00000146476 ∙ NCBI:79624 ∙ OMIM:616332 ∙ HGNC:17872 ∙ Uniprot:Q9H993 ∙ 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 ARMT1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ARMT1 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			26			26
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	26	0	0

Variants in ARMT1

This is a list of pathogenic ClinVar variants found in the ARMT1 region.

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

Position	Type	Phenotype	Significance	ClinVar
6-151458355-A-G		not specified	Uncertain significance (Jun 06, 2023)
6-151458405-T-A		not specified	Uncertain significance (Oct 03, 2024)
6-151458436-G-A		not specified	Uncertain significance (Aug 04, 2021)
6-151458439-A-G		not specified	Uncertain significance (Aug 28, 2023)
6-151458484-A-C		not specified	Uncertain significance (Oct 25, 2023)
6-151458515-C-T		not specified	Uncertain significance (Aug 10, 2021)
6-151458519-G-T		not specified	Uncertain significance (Jan 31, 2024)
6-151458553-C-A		not specified	Uncertain significance (Sep 10, 2024)
6-151464478-T-C		not specified	Uncertain significance (May 11, 2022)
6-151464538-A-G		not specified	Uncertain significance (Jun 28, 2024)
6-151464541-C-T		not specified	Likely benign (Aug 06, 2024)
6-151468377-T-C		not specified	Uncertain significance (Aug 05, 2024)
6-151468386-G-A		not specified	Uncertain significance (Jan 03, 2024)
6-151468565-A-G		not specified	Uncertain significance (Dec 07, 2023)
6-151468637-A-G		not specified	Uncertain significance (Aug 17, 2022)
6-151468661-A-G		not specified	Uncertain significance (Nov 09, 2023)
6-151468664-A-G		not specified	Uncertain significance (Feb 27, 2023)
6-151468702-C-A		not specified	Uncertain significance (Jul 12, 2022)
6-151468720-G-A		not specified	Uncertain significance (Jun 01, 2023)
6-151468772-T-A		not specified	Uncertain significance (Apr 20, 2023)
6-151468803-A-G		not specified	Uncertain significance (Oct 13, 2023)
6-151468805-G-A		not specified	Uncertain significance (Aug 21, 2023)
6-151468807-G-T		not specified	Uncertain significance (Jan 24, 2024)
6-151468815-C-G		not specified	Uncertain significance (Feb 17, 2022)
6-151468817-A-G		not specified	Uncertain significance (Dec 16, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ARMT1	protein_coding	protein_coding	ENST00000367294	5	17815

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
5.12e-7	0.863	125651	0	97	125748	0.000386

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.481	200	220	0.909	0.0000102	2895
Missense in Polyphen		49	63.879	0.76708		832
Synonymous	0.654	76	83.6	0.909	0.00000421	797
Loss of Function	1.54	13	20.5	0.633	9.99e-7	257

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000764	0.000757
Ashkenazi Jewish	0.000698	0.000695
East Asian	0.000382	0.000381
Finnish	0.00	0.00
European (Non-Finnish)	0.000536	0.000519
Middle Eastern	0.000382	0.000381
South Asian	0.000248	0.000229
Other	0.000173	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: O-methyltransferase that methylates glutamate residues of target proteins to form gamma-glutamyl methyl ester residues. Methylates PCNA, suggesting it is involved in the DNA damage response. {ECO:0000269|PubMed:25732820}.

Recessive Scores

• pRec: 0.0882

Intolerance Scores

• rvis_EVS: 0.28
• rvis_percentile_EVS: 71.41

Haploinsufficiency Scores

• pHI: 0.629
• hipred: N
• hipred_score: 0.251
• ghis: 0.540

Essentials

• essential_gene_gene_trap: N

Mouse Genome Informatics

• Gene name: Armt1

Gene ontology

• Biological process: protein methylation;cellular response to DNA damage stimulus;methylation;regulation of response to DNA damage stimulus
• Molecular function: protein binding;S-adenosylmethionine-dependent methyltransferase activity;enzyme binding;protein carboxyl O-methyltransferase activity