ARMH3

protein-coding

armadillo like helical domain containing 3, the group of Armadillo like helical domain containing

Gene summary

Involved in regulation of Golgi organization. Located in Golgi membrane and cytosol. [provided by Alliance of Genome Resources, Jul 2025]

Previous symbols:

C10orf76

MANE transcript

NM_024541.3

Inheritance

—

ClinVar variants

U:8B:1

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.38

Max pathogenic AF

—

Genomic locus

chr10:101,845,599-102,056,193

External References & Databases

Ensembl (ENSG00000120029)

Transcript & Mutation Effects

hg38 • Region Span ~210.6 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 ARMH3 variants in ClinVar

1 Conditions Cataloged

not providedTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_024541.3. 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			4 clinvar	1 clinvar		5
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			3 clinvar			3
Total	0	0	8	1	0	9

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 90 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_024541.3	RefSeq	NP_078817.2	25	MANE Select
ENST00000370033.9	Ensembl	ENSP00000359050.4	25	MANE Select
ENST00000311122.5	Ensembl	ENSP00000312408.4	4	Standard
ENST00000311122.6	Ensembl	ENSP00000312408.4	4	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Molecular Function

protein binding

Cellular Component

integral component of membrane

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000370033
Coding exons: 25
Length: 210595
Individuals with no LoFs: 124758
Homozygous LoFs: 0
Heterozygous LoFs: 37
Defined: 124795
p: 0.000148

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	2.01	271	382	0.710	0.0000199	4579
Missense (PolyPhen)		66	110	0.60002		1330
Synonymous	0.693	125	135	0.924	0.00000685	1246
Loss of Function	3.82	17	44.5	0.382	0.00000219	543

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00013	0.00013	rare
Latino/Admixed American	0.000087	0.000087	rare
Ashkenazi Jewish	0.0014	0.0014	notable
East Asian	0.00011	0.00011	rare
Finnish	0	0.0	absent
European (Non-Finnish)	0.000089	0.000088	rare
South Asian	0.00013	0.00013	rare
Other	0.00033	0.00033	rare

dbNSFP Gene Annotations

Source: dbNSFP

Recessive Scores

pRec: 0.0932

Intolerance Scores

RVIS EVS: -0.43
RVIS percentile EVS: 25.37

Essentials

Essential (gene trap): K