ARVCF

protein-coding

ARVCF delta catenin family member, the group of Armadillo like helical domain containing|p120 catenin family|Armadillo repeat containing

Gene summary

Armadillo Repeat gene deleted in Velo-Cardio-Facial syndrome (ARVCF) is a member of the catenin family. This family plays an important role in the formation of adherens junction complexes, which are thought to facilitate communication between the inside and outside environments of a cell. The ARVCF gene was isolated in the search for the genetic defect responsible for the autosomal dominant Velo-Cardio-Facial syndrome (VCFS), a relatively common human disorder with phenotypic features including cleft palate, conotruncal heart defects and facial dysmorphology. The ARVCF gene encodes a protein containing two motifs, a coiled coil domain in the N-terminus and a 10 armadillo repeat sequence in the midregion. Since these sequences can facilitate protein-protein interactions ARVCF is thought to function in a protein complex. In addition, ARVCF contains a predicted nuclear-targeting sequence suggesting that it may have a function as a nuclear protein. [provided by RefSeq, Jun 2010]

MANE transcript

NM_001670.3

Inheritance

—

ClinVar variants

U:230B:33

Top phenotype

Long QT syndrome

gnomAD constraint

pLI —, LoF o/e 0.58

Max pathogenic AF

—

Genomic locus

chr22:19,969,896-20,016,823

External References & Databases

Ensembl (ENSG00000099889)

Transcript & Mutation Effects

hg38 • Region Span ~46.9 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 ARVCF variants in ClinVar

5 Conditions Cataloged

not specifiedTotal: 214

not providedTotal: 44

Long QT syndromeTotal: 1

MicrocephalyTotal: 1

See casesTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_001670.3. 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	13 clinvar	6 clinvar	20
missense			222 clinvar	9 clinvar	5 clinvar	236
nonsense						0
start loss						0
frameshift			3 clinvar			3
splice donor/acceptor (+/-2bp)			4 clinvar			4
Total	0	0	230	22	11	263

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 45 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_001670.3	RefSeq	NP_001661.1	17	MANE Select
ENST00000263207.8	Ensembl	ENSP00000263207.3	17	MANE Select
NM_001410839.1	RefSeq	NP_001397768.1	16	Standard
NM_001438683.1	RefSeq	NP_001425612.1	16	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

cell-cell junction assembly
cell adhesion
multicellular organism development
calcium-dependent cell-cell adhesion via plasma membrane cell adhesion molecules
cell-cell adhesion

Molecular Function

protein binding
cadherin binding

Cellular Component

nucleus
cytoplasm
plasma membrane
cell-cell junction
cell-cell adherens junction

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000263207
Coding exons: 17
Length: 46913
Individuals with no LoFs: 125555
Homozygous LoFs: 0
Heterozygous LoFs: 187
Defined: 125742
p: 0.000744

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	-0.270	674	655	1.03	0.0000478	6009
Missense (PolyPhen)		276	289.56	0.95316		2709
Synonymous	0.660	279	293	0.951	0.0000215	2140
Loss of Function	2.44	23	39.6	0.581	0.00000199	429

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00013	0.00012	rare
Latino/Admixed American	0.00070	0.00069	rare
Ashkenazi Jewish	0.00064	0.00060	rare
East Asian	0.00029	0.00027	rare
Finnish	0.0042	0.0042	notable
European (Non-Finnish)	0.00041	0.00040	rare
South Asian	0.00043	0.00036	rare
Other	0.00050	0.00049	rare

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: Involved in protein-protein interactions at adherens junctions.;

Recessive Scores

pRec: 0.128

Intolerance Scores

LoFtool: 0.705
RVIS EVS: -0.05
RVIS percentile EVS: 48.95

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: E
Indispensability score: 1.00

Gene Damage Prediction

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