ARMC1

armadillo repeat containing 1, the group of Armadillo repeat containing

Basic information

Region (hg38): 8:65602457-65634217

Links

ENSG00000104442 ∙ NCBI:55156 ∙ ∙ HGNC:17684 ∙ Uniprot:Q9NVT9 ∙ 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 ARMC1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ARMC1 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				1		1
missense			10			10
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	10	1	0

Variants in ARMC1

This is a list of pathogenic ClinVar variants found in the ARMC1 region.

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

Position	Type	Phenotype	Significance	ClinVar
8-65604467-C-T		not specified	Uncertain significance (Oct 27, 2021)
8-65604471-C-G		not specified	Uncertain significance (Sep 01, 2021)
8-65613245-G-A		not specified	Uncertain significance (Nov 08, 2022)
8-65613330-G-A		not specified	Uncertain significance (Nov 17, 2022)
8-65613342-C-T		not specified	Uncertain significance (Jan 03, 2024)
8-65627233-C-T		not specified	Uncertain significance (Apr 13, 2022)
8-65627266-T-C		not specified	Uncertain significance (Oct 05, 2021)
8-65627295-A-C		not specified	Uncertain significance (Dec 05, 2022)
8-65627296-C-T		not specified	Uncertain significance (Jan 30, 2024)
8-65627352-G-A		not specified	Uncertain significance (Jul 26, 2022)
8-65627387-G-A			Likely benign (Mar 01, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ARMC1	protein_coding	protein_coding	ENST00000276569	6	31749

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.763	0.237	125730	0	6	125736	0.0000239

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.32	113	160	0.706	0.00000906	1834
Missense in Polyphen		13	31	0.41935		398
Synonymous	-0.511	60	55.2	1.09	0.00000301	550
Loss of Function	2.90	2	13.5	0.148	7.96e-7	162

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000907	0.0000904
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000544	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.0000272	0.0000264
Middle Eastern	0.0000544	0.0000544
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Recessive Scores

• pRec: 0.124

Intolerance Scores

• loftool: 0.360
• rvis_EVS: -0.32
• rvis_percentile_EVS: 31.46

Haploinsufficiency Scores

• pHI: 0.219
• hipred: Y
• hipred_score: 0.696
• ghis: 0.687

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.326

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Armc1

Gene ontology

• Biological process: metal ion transport
• Molecular function: protein binding;metal ion binding