GJC1

protein-coding

gap junction protein gamma 1, the group of Gap junction proteins

Gene summary

This gene is a member of the connexin gene family. The encoded protein is a component of gap junctions, which are composed of arrays of intercellular channels that provide a route for the diffusion of low molecular weight materials from cell to cell. Alternatively spliced transcript variants encoding the same isoform have been described. [provided by RefSeq, Jul 2008]

Previous symbols:

GJA7

MANE transcript

NM_005497.4

Inheritance

—

ClinVar variants

U:30B:4

Top phenotype

EBV-positive nodal T- and NK-cell lymphoma

gnomAD constraint

pLI —, LoF o/e 0

Max pathogenic AF

—

Genomic locus

chr17:44,798,448-44,830,816

External References & Databases

Ensembl (ENSG00000182963)

Transcript & Mutation Effects

hg38 • Region Span ~32.4 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 GJC1 variants in ClinVar

3 Conditions Cataloged

not specifiedTotal: 30

not providedTotal: 2

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

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_005497.4. 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		2 clinvar	3
missense			29 clinvar	2 clinvar		31
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	30	2	2	34

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 43 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_005497.4	RefSeq	NP_005488.2	1	MANE Select
ENST00000592524.6	Ensembl	ENSP00000467201.1	1	MANE Select
NM_001080383.2	RefSeq	NP_001073852.1	1	Standard
ENST00000330514.4	Ensembl	ENSP00000333193.3	1	Standard

Model Organisms & Knockout Phenotypes

Observed phenotypic effects in mouse and zebrafish models

Gene / Model	Organism	Observed Phenotype
cx43.4	Danio rerio	Structure: pancreatic bud Quality: mislocalised radially abnormal

Gene / Model

Organism

Observed Phenotype

cx43.4

Danio rerio

Structure: pancreatic bud

Quality: mislocalised radially

abnormal

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

Calcium Regulation in the Cardiac Cell
Electric Transmission Across Gap Junctions
Transmission across Electrical Synapses
Neuronal System

Biological Process

vasculogenesis
muscle contraction
cell-cell junction assembly
chemical synaptic transmission
visual perception

Molecular Function

ion channel activity
gap junction channel activity involved in SA node cell-atrial cardiac muscle cell electrical coupling
gap junction channel activity involved in AV node cell-bundle of His cell electrical coupling

Cellular Component

endoplasmic reticulum membrane
plasma membrane
gap junction
connexin complex
intercalated disc

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000426548
Coding exons: 1
Length: 32369
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	2.07	135	222	0.608	0.0000130	2626
Missense (PolyPhen)		35	94.384	0.37083		1140
Synonymous	0.313	81	84.7	0.957	0.00000485	764
Loss of Function	3.38	0	13.3	0.00	8.33e-7	150

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.;

Recessive Scores

pRec: 0.175

Intolerance Scores

LoFtool: 0.0404
RVIS EVS: -0.12
RVIS percentile EVS: 44.89

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.373

Gene Damage Prediction

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