ARMC1

protein-coding

armadillo repeat containing 1, the group of Armadillo repeat containing

Gene summary

Predicted to enable metal ion binding activity. Involved in intracellular distribution of mitochondria. Located in cytosol and mitochondrion. [provided by Alliance of Genome Resources, Jul 2025]

MANE transcript

NM_018120.6

Inheritance

—

ClinVar variants

U:38B:1

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.15

Max pathogenic AF

—

Genomic locus

chr8:65,602,458-65,634,217

External References & Databases

Ensembl (ENSG00000104442)

Transcript & Mutation Effects

hg38 • Region Span ~31.8 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to ARMC1 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 32

not providedTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_018120.6. 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			3 clinvar	1 clinvar		4
missense			32 clinvar			32
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			3 clinvar			3
Total	0	0	38	1	0	39

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 32 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_018120.6	RefSeq	NP_060590.1	6	MANE Select
ENST00000276569.8	Ensembl	ENSP00000276569.3	6	MANE Select
NM_001286702.2	RefSeq	NP_001273631.1	5	Standard
ENST00000458464.3	Ensembl	ENSP00000388572.2	5	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

metal ion transport

Molecular Function

protein binding
metal ion binding

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000276569
Coding exons: 6
Length: 31749
Individuals with no LoFs: 125730
Homozygous LoFs: 0
Heterozygous LoFs: 6
Defined: 125736
p: 0.0000239

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	1.32	113	160	0.706	0.00000906	1834
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0.000062	0.000062	rare
Latino/Admixed American	0.000029	0.000029	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0.000054	0.000054	rare
Finnish	0	0.0	absent
European (Non-Finnish)	0.000027	0.000026	rare
South Asian	0	0.0	absent
Other	0	0.0	absent

dbNSFP Gene Annotations

Source: dbNSFP

Recessive Scores

pRec: 0.124

Intolerance Scores

LoFtool: 0.360
RVIS EVS: -0.32
RVIS percentile EVS: 31.46

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.326

Gene Damage Prediction

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