ARMC10

protein-coding

armadillo repeat containing 10, the group of Armadillo repeat containing

Gene summary

This gene encodes a protein that contains an armadillo repeat and transmembrane domain. The encoded protein decreases the transcriptional activity of the tumor suppressor protein p53 through direct interaction with the DNA-binding domain of p53, and may play a role in cell growth and survival. Upregulation of this gene may play a role in hepatocellular carcinoma. Alternatively spliced transcript variants encoding multiple isoforms have been observed for this gene, and a pseudogene of this gene is located on the long arm of chromosome 3. [provided by RefSeq, Sep 2011]

MANE transcript

NM_031905.5

Inheritance

—

ClinVar variants

U:53B:2

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.61

Max pathogenic AF

—

Genomic locus

chr7:103,074,881-103,099,759

External References & Databases

Ensembl (ENSG00000170632)

Transcript & Mutation Effects

hg38 • Region Span ~24.9 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 ARMC10 variants in ClinVar

1 Conditions Cataloged

not specifiedTotal: 52

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_031905.5. 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						0
missense			51 clinvar	2 clinvar		53
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			2 clinvar			2
Total	0	0	53	2	0	55

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 113 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_031905.5	RefSeq	NP_114111.2	7	MANE Select
ENST00000323716.8	Ensembl	ENSP00000319412.3	7	MANE Select
NM_001161009.3	RefSeq	NP_001154481.1	6	Standard
NM_001161010.3	RefSeq	NP_001154482.1	6	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

regulation of growth

Cellular Component

mitochondrion
endoplasmic reticulum
endoplasmic reticulum membrane
integral component of membrane

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000323716
Coding exons: 7
Length: 24878
Individuals with no LoFs: 125663
Homozygous LoFs: 0
Heterozygous LoFs: 84
Defined: 125747
p: 0.000334

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.353	139	151	0.919	0.00000725	2155
Missense (PolyPhen)		48	57.394	0.83632		837
Synonymous	0.154	58	59.5	0.975	0.00000293	684
Loss of Function	1.32	8	13.2	0.608	6.20e-7	184

Population LoF Frequency

Population	CAF	p-value	Status
African	0.000062	0.000062	rare
Latino/Admixed American	0.000071	0.000058	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0.0026	0.0026	notable
Finnish	0	0.0	absent
European (Non-Finnish)	0.00017	0.00017	rare
South Asian	0.00043	0.00042	rare
Other	0.00018	0.00016	rare

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: May play a role in cell survival and cell growth. May suppress the transcriptional activity of p53/TP53. {ECO:0000269|PubMed:12839973, ECO:0000269|PubMed:17904127}.;

Recessive Scores

pRec: 0.106

Intolerance Scores

LoFtool: 0.936
RVIS EVS: 0.13
RVIS percentile EVS: 63.2

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: E
Indispensability score: 0.548

Gene Damage Prediction

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