ARMC12

protein-coding

armadillo repeat containing 12, the group of Armadillo repeat containing

Gene summary

Involved in positive regulation of cell growth and sperm mitochondrial sheath assembly. Located in mitochondrion and nucleus. Implicated in spermatogenic failure 90. [provided by Alliance of Genome Resources, Jun 2026]

Previous symbols:

C6orf81

MANE transcript

NM_001286574.2

Inheritance

ClinVar variants

P:3U:54B:1

Top phenotype

Spermatogenic failure 90

gnomAD constraint

pLI —, LoF o/e 0.65

Max pathogenic AF

—

Genomic locus

chr6:35,737,032-35,749,079

External References & Databases

Ensembl (ENSG00000157343)

Transcript & Mutation Effects

hg38 • Region Span ~12.0 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

Clinical Genomic Database (CGD)

Spermatogenic failure 90AR

Manifestation: Genitourinary

Intervention: General

Rationale: 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

Refs: 35534203

Source: CGD (NHGRI)

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to ARMC12 variants in ClinVar

4 Conditions Cataloged

not specifiedTotal: 55

Spermatogenic failure 90Total: 3

not providedTotal: 2

Prostate cancerTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_001286574.2. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous				1 clinvar		1
missense	3 clinvar		54 clinvar			57
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	3	0	54	1	0	58

Highest pathogenic variant AF is 0.00006815805

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 20 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_001286574.2	RefSeq	NP_001273503.1	6	MANE Select
ENST00000373866.4	Ensembl	ENSP00000362973.3	6	MANE Select
NM_001286576.2	RefSeq	NP_001273505.1	6	Standard
NM_145028.5	RefSeq	NP_659465.2	6	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Cellular Component

nucleus

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000288065
Coding exons: 6
Length: 12048
Individuals with no LoFs: 125684
Homozygous LoFs: 0
Heterozygous LoFs: 64
Defined: 125748
p: 0.000255

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.272	206	217	0.948	0.0000131	2355
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00031	0.00031	rare
Latino/Admixed American	0.00023	0.00023	rare
Ashkenazi Jewish	0.00030	0.00030	rare
East Asian	0.000054	0.000054	rare
Finnish	0.000046	0.000046	rare
European (Non-Finnish)	0.00036	0.00036	rare
South Asian	0.000065	0.000065	rare
Other	0.00049	0.00049	rare

dbNSFP Gene Annotations

Source: dbNSFP

Intolerance Scores

RVIS EVS: -0.07
RVIS percentile EVS: 48.78

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.114

Gene Damage Prediction

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