ARMC3

armadillo repeat containing 3, the group of Armadillo repeat containing

Basic information

Region (hg38): 10:22928023-23038523

Links

ENSG00000165309 ∙ NCBI:219681 ∙ OMIM:611226 ∙ HGNC:30964 ∙ Uniprot:Q5W041 ∙ 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 ARMC3 gene.

• Inborn genetic diseases (40 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ARMC3 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			38	1		39
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region				1		1
non coding						0
Total	0	0	38	1	0

Variants in ARMC3

This is a list of pathogenic ClinVar variants found in the ARMC3 region.

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

Position	Type	Phenotype	Significance	ClinVar
10-22932016-A-C		not specified	Uncertain significance (Jun 22, 2023)
10-22946181-C-G		not specified	Uncertain significance (Feb 23, 2023)
10-22946194-G-A		not specified	Uncertain significance (Jan 17, 2023)
10-22955849-A-G		not specified	Uncertain significance (Oct 12, 2022)
10-22955903-C-T		not specified	Uncertain significance (Jun 09, 2022)
10-22959407-G-C		not specified	Uncertain significance (Jan 02, 2024)
10-22959491-T-A		not specified	Uncertain significance (Nov 10, 2022)
10-22959528-C-T		not specified	Uncertain significance (Sep 12, 2023)
10-22959546-C-T		not specified	Uncertain significance (Sep 26, 2022)
10-22961920-G-T		not specified	Uncertain significance (Oct 10, 2023)
10-22961978-C-T		not specified	Uncertain significance (Jan 20, 2023)
10-22962058-A-G		not specified	Uncertain significance (Dec 06, 2021)
10-22968351-T-A		not specified	Uncertain significance (Jan 02, 2024)
10-22968448-A-G		not specified	Uncertain significance (Jan 02, 2024)
10-22968475-A-G		not specified	Uncertain significance (Aug 14, 2023)
10-22968490-G-A		Stuttering, familial persistent, 4	Uncertain significance (Jul 07, 2022)
10-22981387-G-T		not specified	Uncertain significance (Dec 18, 2023)
10-22981403-C-T		not specified	Uncertain significance (Feb 13, 2023)
10-22981426-G-A		not specified	Uncertain significance (Aug 12, 2021)
10-22981475-A-T		not specified	Uncertain significance (Dec 27, 2023)
10-22981490-A-T		not specified	Uncertain significance (Oct 10, 2023)
10-22981603-C-G		not specified	Uncertain significance (Sep 16, 2021)
10-22981642-C-T		not specified	Likely benign (Jul 25, 2023)
10-22998148-C-T		not specified	Likely benign (Jul 19, 2023)
10-22998152-G-T		not specified	Uncertain significance (May 26, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ARMC3	protein_coding	protein_coding	ENST00000298032	18	109566

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
3.54e-13	0.899	125553	1	194	125748	0.000776

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.910	400	455	0.880	0.0000234	5698
Missense in Polyphen		107	146.14	0.73215		1953
Synonymous	1.21	144	164	0.880	0.00000889	1658
Loss of Function	2.03	26	39.8	0.653	0.00000215	533

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000818	0.000818
Ashkenazi Jewish	0.00	0.00
East Asian	0.00430	0.00403
Finnish	0.000602	0.000601
European (Non-Finnish)	0.000393	0.000387
Middle Eastern	0.00430	0.00403
South Asian	0.00137	0.00124
Other	0.00119	0.00114

dbNSFP

Source: dbNSFP

Recessive Scores

• pRec: 0.0986

Intolerance Scores

• loftool: 0.951
• rvis_EVS: 0.56
• rvis_percentile_EVS: 81.67

Haploinsufficiency Scores

• pHI: 0.159
• hipred: N
• hipred_score: 0.429

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.126

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Armc3

Gene ontology

• Cellular component: extracellular exosome