GJD3

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

Basic information

Region (hg38): 17:40360652-40364737

Previous symbols: [ "GJC1" ]

Links

ENSG00000183153 ∙ NCBI:125111 ∙ OMIM:607425 ∙ HGNC:19147 ∙ Uniprot:Q8N144 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the GJD3 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the GJD3 gene is commonly pathogenic or not.

In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.

Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.

Variant type	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous				2		2
missense			30	2		32
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	30	4	0

Variants in GJD3

This is a list of pathogenic ClinVar variants found in the GJD3 region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
17-40362980-C-A		not specified	Uncertain significance (Oct 20, 2024)
17-40362993-C-T		not specified	Uncertain significance (Feb 11, 2022)
17-40362996-G-A		not specified	Uncertain significance (Oct 12, 2024)
17-40363029-G-A		not specified	Uncertain significance (Feb 28, 2025)
17-40363058-C-G		Meniere disease	Likely benign (Jan 09, 2024)
17-40363065-G-T		not specified	Uncertain significance (Apr 23, 2024)
17-40363098-G-A		not specified	Uncertain significance (Mar 07, 2023)
17-40363115-G-A		not specified	Uncertain significance (Jul 20, 2021)
17-40363131-G-T		not specified	Uncertain significance (Sep 27, 2021)
17-40363161-G-T		not specified	Uncertain significance (Feb 09, 2025)
17-40363181-A-G		not specified	Uncertain significance (Dec 26, 2023)
17-40363184-T-C		not specified	Uncertain significance (Aug 22, 2023)
17-40363235-T-C		not specified	Uncertain significance (Dec 22, 2023)
17-40363256-T-G		not specified	Uncertain significance (Nov 02, 2023)
17-40363280-C-A		not specified	Uncertain significance (Jan 27, 2022)
17-40363293-G-A		Meniere disease	Likely benign (Jan 09, 2024)
17-40363294-C-G		Meniere disease	Likely benign (Jan 09, 2024)
17-40363325-G-A		not specified	Uncertain significance (Aug 22, 2023)
17-40363377-C-T		not specified	Uncertain significance (Jun 28, 2022)
17-40363380-C-G		not specified	Uncertain significance (Nov 13, 2024)
17-40363412-C-T		not specified	Uncertain significance (Dec 31, 2023)
17-40363416-G-C		not specified	Uncertain significance (Feb 24, 2025)
17-40363418-C-A		not specified	Uncertain significance (May 14, 2024)
17-40363425-G-A		not specified	Uncertain significance (Oct 03, 2022)
17-40363527-T-A		not specified	Uncertain significance (Sep 16, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
GJD3	protein_coding	protein_coding	ENST00000578689	1	2833

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0000335	0.211	0	0	0	0	0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.761	71	91.5	0.776	0.00000425	1772
Missense in 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

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.00	0.00
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

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}.
• Pathway: Antiarrhythmic Pathway, Pharmacodynamics (Consensus)

Recessive Scores

• pRec: 0.0948

Haploinsufficiency Scores

• pHI: 0.428
• hipred: N
• hipred_score: 0.324
• ghis: 0.517

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.822

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Gjd3
• Phenotype: cardiovascular system phenotype (the observable morphological and physiological characteristics of the mammalian heart, blood vessels, or circulatory system that are manifested through development and lifespan)

Gene ontology

• Biological process: cell communication;response to glucose;gap junction assembly;ion transmembrane transport;cell communication by electrical coupling involved in cardiac conduction;cell communication involved in cardiac conduction
• Cellular component: integral component of plasma membrane;connexin complex;cell surface
• Molecular function: ion channel activity;protein binding;gap junction channel activity involved in cardiac conduction electrical coupling