GJD4

protein-coding

gap junction protein delta 4, the group of Gap junction proteins

Gene summary

Connexins, such as GJD4, are involved in the formation of gap junctions, intercellular conduits that directly connect the cytoplasms of contacting cells. Each gap junction channel is formed by docking of 2 hemichannels, each of which contains 6 connexin subunits (Sohl et al., 2003 [PubMed 12881038]).[supplied by OMIM, Mar 2008]

MANE transcript

NM_153368.3

Inheritance

—

ClinVar variants

U:75B:7

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 1.73

Max pathogenic AF

—

Genomic locus

chr10:35,605,341-35,608,935

External References & Databases

Ensembl (ENSG00000177291)

Transcript & Mutation Effects

hg38 • Region Span ~3.6 kb

Loading mutation effect viewer...

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 GJD4 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 79

not providedTotal: 3

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_153368.3. 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				2 clinvar		2
missense			75 clinvar	4 clinvar	1 clinvar	80
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	75	6	1	82

Loading ClinVar variants...

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_153368.3	RefSeq	NP_699199.2	2	MANE Select
ENST00000321660.2	Ensembl	ENSP00000315070.1	2	MANE Select

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

cell communication
regulation of satellite cell activation involved in skeletal muscle regeneration

Cellular Component

connexin complex
integral component of membrane

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000321660
Coding exons: 2
Length: 3526
Individuals with no LoFs: 125556
Homozygous LoFs: 0
Heterozygous LoFs: 148
Defined: 125704
p: 0.000589

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	-1.01	266	224	1.19	0.0000149	2264
Missense (PolyPhen)		90	66.58	1.3518		754
Synonymous	-2.16	143	114	1.26	0.00000832	848
Loss of Function	-0.725	2	1.16	1.73	4.92e-8	13

Population LoF Frequency

Population	CAF	p-value	Status
African	0.000062	0.000062	rare
Latino/Admixed American	0.000029	0.000029	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0.0071	0.0071	notable
Finnish	0	0.0	absent
European (Non-Finnish)	0	0.0	absent
South Asian	0.00049	0.00049	rare
Other	0.00016	0.00016	rare

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: 0.0994

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.0151

Gene Damage Prediction

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