ARMC2

armadillo repeat containing 2, the group of Armadillo repeat containing

Basic information

Region (hg38): 6:108848415-108974476

Links

ENSG00000118690 ∙ NCBI:84071 ∙ OMIM:618424 ∙ HGNC:23045 ∙ Uniprot:Q8NEN0 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• spermatogenic failure 38 (Strong), mode of inheritance: AR
• non-syndromic male infertility due to sperm motility disorder (Supportive), mode of inheritance: AR
• spermatogenic failure 38 (Definitive), mode of inheritance: AR

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Spermatogenic failure 38	AR	General	Genetic knowledge may be beneficial related to issues such as selection of optimal supportive care, informed medical decision-making, prognostic considerations, and avoidance of unnecessary testing	Genitourinary	30686508

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the ARMC2 gene.

• Inborn genetic diseases (24 variants)
• not provided (3 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ARMC2 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				3		3
missense			22	2		24
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	22	5	0

Variants in ARMC2

This is a list of pathogenic ClinVar variants found in the ARMC2 region.

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

Position	Type	Phenotype	Significance	ClinVar
6-108854301-C-G		not specified	Uncertain significance (Mar 22, 2022)
6-108854352-A-T		not specified	Uncertain significance (Dec 16, 2022)
6-108854422-A-C		ARMC2-related disorder	Benign (Nov 20, 2019)
6-108854481-T-C		not specified	Uncertain significance (May 26, 2023)
6-108858195-C-T		ARMC2-related disorder	Benign (Dec 02, 2019)
6-108858233-A-G		not specified	Uncertain significance (Aug 02, 2023)
6-108858251-C-T		not specified	Uncertain significance (Dec 19, 2022)
6-108868829-G-A		ARMC2-related disorder	Benign (Jan 20, 2020)
6-108868852-G-A		not specified	Uncertain significance (Jun 24, 2022)
6-108868891-T-A		not specified	Uncertain significance (Jan 07, 2022)
6-108868900-C-T		not specified	Uncertain significance (Nov 09, 2023)
6-108868937-A-G			Likely benign (May 01, 2023)
6-108868940-C-T			Likely benign (May 01, 2023)
6-108868941-A-G			Uncertain significance (-)
6-108868942-G-A		not specified	Uncertain significance (May 22, 2023)
6-108868953-C-T		Spermatogenic failure 38 • Male infertility with teratozoospermia due to single gene mutation	Pathogenic (May 15, 2019)
6-108868969-C-T		not specified	Uncertain significance (Oct 14, 2023)
6-108876176-T-C		ARMC2-related disorder	Benign (Nov 11, 2019)
6-108876230-C-T		ARMC2-related disorder	Benign (Dec 06, 2019)
6-108876232-A-G			Uncertain significance (-)
6-108876333-T-G			Likely benign (Aug 01, 2022)
6-108876335-A-G		not specified	Uncertain significance (Feb 23, 2023)
6-108899744-G-T		not specified	Uncertain significance (Feb 15, 2023)
6-108899769-C-T		not specified	Uncertain significance (Jan 05, 2022)
6-108899778-G-A		not specified	Likely benign (Mar 03, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ARMC2	protein_coding	protein_coding	ENST00000392644	17	125568

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
2.48e-9	0.994	125508	0	85	125593	0.000338

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.736	409	453	0.903	0.0000239	5661
Missense in Polyphen		89	118.49	0.75111		1499
Synonymous	-0.940	198	182	1.09	0.0000105	1670
Loss of Function	2.56	20	36.8	0.544	0.00000165	526

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000369	0.000369
Ashkenazi Jewish	0.00	0.00
East Asian	0.000342	0.000326
Finnish	0.0000462	0.0000462
European (Non-Finnish)	0.000515	0.000502
Middle Eastern	0.000342	0.000326
South Asian	0.000400	0.000392
Other	0.000163	0.000163

dbNSFP

Source: dbNSFP

Recessive Scores

• pRec: 0.0834

Intolerance Scores

• loftool: 0.948
• rvis_EVS: -0.55
• rvis_percentile_EVS: 19.93

Haploinsufficiency Scores

• pHI: 0.0906
• hipred: N
• hipred_score: 0.169
• ghis: 0.495

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.0650

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Armc2

Gene ontology

• Molecular function: protein binding