ARMC12

armadillo repeat containing 12, the group of Armadillo repeat containing

Basic information

Region (hg38): 6:35737032-35749079

Previous symbols: [ "C6orf81" ]

Links

ENSG00000157343 ∙ NCBI:221481 ∙ ∙ HGNC:21099 ∙ Uniprot:Q5T9G4 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Spermatogenic failure 90	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	35534203

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the ARMC12 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ARMC12 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			17			17
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	17	1	0

Variants in ARMC12

This is a list of pathogenic ClinVar variants found in the ARMC12 region.

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

Position	Type	Phenotype	Significance	ClinVar
6-35737151-C-T		not specified	Uncertain significance (Dec 01, 2022)
6-35737160-G-A		not specified	Uncertain significance (Mar 05, 2024)
6-35737290-G-C		not specified	Uncertain significance (Jul 19, 2023)
6-35737299-C-T			Uncertain significance (-)
6-35737309-G-C		not specified	Uncertain significance (Nov 07, 2022)
6-35738048-G-A		not specified	Uncertain significance (Aug 02, 2023)
6-35738057-G-A		not specified	Uncertain significance (Apr 07, 2023)
6-35738076-G-A			Likely benign (Feb 01, 2023)
6-35738385-C-T		not specified	Uncertain significance (Feb 24, 2023)
6-35738396-A-G		not specified	Uncertain significance (May 28, 2024)
6-35738400-C-T		not specified	Uncertain significance (Dec 06, 2023)
6-35738420-G-A		not specified	Uncertain significance (Aug 17, 2021)
6-35747274-A-T		not specified	Uncertain significance (Oct 29, 2021)
6-35747276-G-C		not specified	Uncertain significance (Apr 26, 2024)
6-35747282-G-A		not specified	Uncertain significance (Aug 11, 2022)
6-35747357-G-A		not specified	Uncertain significance (Apr 15, 2024)
6-35747358-A-G		not specified	Uncertain significance (Mar 22, 2023)
6-35747417-G-T		Malignant tumor of prostate	Uncertain significance (-)
6-35747589-G-A		Spermatogenic failure 90	Pathogenic (Mar 01, 2024)
6-35747592-T-C		Spermatogenic failure 90	Pathogenic (Mar 01, 2024)
6-35747643-G-A		Spermatogenic failure 90	Pathogenic (Mar 01, 2024)
6-35748631-C-T		not specified	Uncertain significance (May 23, 2023)
6-35748710-C-T		not specified	Uncertain significance (Dec 07, 2021)
6-35748785-T-C		not specified	Uncertain significance (Apr 07, 2022)
6-35748827-C-A		not specified	Uncertain significance (Apr 26, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ARMC12	protein_coding	protein_coding	ENST00000288065	6	12048

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00000116	0.817	125684	0	64	125748	0.000255

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.272	206	217	0.948	0.0000131	2355
Missense in Polyphen		64	74.674	0.85706		879
Synonymous	-0.171	93	90.9	1.02	0.00000529	760
Loss of Function	1.39	12	18.5	0.650	0.00000123	175

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000539	0.000539
Ashkenazi Jewish	0.000298	0.000298
East Asian	0.0000544	0.0000544
Finnish	0.0000463	0.0000462
European (Non-Finnish)	0.000361	0.000360
Middle Eastern	0.0000544	0.0000544
South Asian	0.0000653	0.0000653
Other	0.000489	0.000489

dbNSFP

Source: dbNSFP

Intolerance Scores

• rvis_EVS: -0.07
• rvis_percentile_EVS: 48.78

Haploinsufficiency Scores

• pHI: 0.288
• hipred: N
• hipred_score: 0.234
• ghis: 0.429

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.114

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Armc12

Gene ontology

• Cellular component: nucleus