GJD3

protein-coding

gap junction protein delta 3, the group of Gap junction proteins

Gene summary

This gene is a member of the large family of connexins that are required for the formation of gap junctions. Six connexin monomers form a hemichannel, or connexon, on the cell surface. This connexon can interact with a connexon from a neighboring cell, thus forming a channel linking the cytoplasm of the 2 cells. [provided by RefSeq, Jul 2008]

Previous symbols:

GJC1

MANE transcript

NM_152219.4

Inheritance

—

ClinVar variants

U:57B:1

Top phenotype

Meniere disease

gnomAD constraint

pLI —, LoF o/e 1.3

Max pathogenic AF

—

Genomic locus

chr17:40,360,652-40,364,737

External References & Databases

Ensembl (ENSG00000183153)

Transcript & Mutation Effects

hg38 • Region Span ~4.1 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 GJD3 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 57

Meniere diseaseTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_152219.4. 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			57 clinvar			57
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	57	1	0	58

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 2 of 2 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_152219.4	RefSeq	NP_689343.3	1	MANE Select
ENST00000578689.2	Ensembl	ENSP00000463752.1	1	MANE Select

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

Antiarrhythmic Pathway, Pharmacodynamics

Biological Process

cell communication
response to glucose
gap junction assembly
ion transmembrane transport
cell communication by electrical coupling involved in cardiac conduction

Molecular Function

ion channel activity
protein binding
gap junction channel activity involved in cardiac conduction electrical coupling

Cellular Component

integral component of plasma membrane
connexin complex
cell surface

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000578689
Coding exons: 1
Length: 2833
Individuals with no LoFs: 0
Homozygous LoFs: 0
Heterozygous LoFs: 0
Defined: 0
p: 0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.761	71	91.5	0.776	0.00000425	1772
Missense (PolyPhen)		32	45.094	0.70964		733
Synonymous	0.372	43	46.2	0.930	0.00000225	676
Loss of Function	-0.598	6	4.61	1.30	2.00e-7	56

Population LoF Frequency

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

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: One gap junction consists of a cluster of closely packed pairs of transmembrane channels, the connexons, through which materials of low MW diffuse from one cell to a neighboring cell. {ECO:0000250}.;

Recessive Scores

pRec: 0.0948

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Indispensability pred.: E
Indispensability score: 0.822

Gene Damage Prediction

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