ARMC3

protein-coding

armadillo repeat containing 3, the group of Armadillo repeat containing

Gene summary

Armadillo/beta-catenin (CTNNB1; MIM 116806)-like (ARM) domains are imperfect 45-amino acid repeats involved in protein-protein interactions. ARM domain-containing proteins, such as ARMC3, function in signal transduction, development, cell adhesion and mobility, and tumor initiation and metastasis (Li et al., 2006 [PubMed 16915934]).[supplied by OMIM, Mar 2008]

MANE transcript

NM_173081.5

Inheritance

—

ClinVar variants

U:127B:5

Top phenotype

EBV-positive nodal T- and NK-cell lymphoma

gnomAD constraint

pLI —, LoF o/e 0.65

Max pathogenic AF

—

Genomic locus

chr10:22,928,024-23,038,523

External References & Databases

Ensembl (ENSG00000165309)

Transcript & Mutation Effects

hg38 • Region Span ~110.5 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 ARMC3 variants in ClinVar

5 Conditions Cataloged

not specifiedTotal: 123

EBV-positive nodal T- and NK-cell lymphomaTotal: 1

not providedTotal: 1

ARMC3-related disorderTotal: 1

Stuttering, familial persistent, 4Total: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_173081.5. 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				3 clinvar		3
missense			120 clinvar	2 clinvar		122
nonsense			2 clinvar			2
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			5 clinvar			5
Total	0	0	127	5	0	132

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 24 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_173081.5	RefSeq	NP_775104.2	18	MANE Select
ENST00000298032.10	Ensembl	ENSP00000298032.5	18	MANE Select
NM_001282745.2	RefSeq	NP_001269674.1	18	Standard
NM_001282746.2	RefSeq	NP_001269675.1	16	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Cellular Component

extracellular exosome

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000298032
Coding exons: 18
Length: 109566
Individuals with no LoFs: 125553
Homozygous LoFs: 1
Heterozygous LoFs: 194
Defined: 125748
p: 0.000776

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.910	400	455	0.880	0.0000234	5698
Missense (PolyPhen)		107	146.14	0.73215		1953
Synonymous	1.21	144	164	0.880	0.00000889	1658
Loss of Function	2.03	26	39.8	0.653	0.00000215	533

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00043	0.00043	rare
Latino/Admixed American	0.00039	0.00035	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0.0043	0.0040	notable
Finnish	0.00060	0.00060	rare
European (Non-Finnish)	0.00039	0.00039	rare
South Asian	0.0014	0.0012	notable
Other	0.0012	0.0011	notable

dbNSFP Gene Annotations

Source: dbNSFP

Recessive Scores

pRec: 0.0986

Intolerance Scores

LoFtool: 0.951
RVIS EVS: 0.56
RVIS percentile EVS: 81.67

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.126

Gene Damage Prediction

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