GJD4

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

Basic information

Region (hg38): 10:35605341-35608935

Links

ENSG00000177291 ∙ NCBI:219770 ∙ OMIM:611922 ∙ HGNC:23296 ∙ Uniprot:Q96KN9 ∙ 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 GJD4 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the GJD4 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				1		1
missense			26	3	1	30
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	26	4	1

Variants in GJD4

This is a list of pathogenic ClinVar variants found in the GJD4 region.

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

Position	Type	Phenotype	Significance	ClinVar
10-35607596-T-C		not specified	Uncertain significance (Jan 23, 2023)
10-35607597-C-A			Likely benign (Oct 01, 2022)
10-35607641-C-A		not specified	Uncertain significance (Sep 26, 2022)
10-35607643-G-A			Benign (May 01, 2022)
10-35607682-C-G		not specified	Uncertain significance (Mar 07, 2023)
10-35607727-G-T		not specified	Uncertain significance (May 01, 2023)
10-35607745-T-G		not specified	Uncertain significance (Jul 30, 2023)
10-35607758-G-A		not specified	Uncertain significance (Apr 23, 2024)
10-35607818-C-T		not specified	Uncertain significance (Dec 20, 2023)
10-35607835-C-T		not specified	Uncertain significance (Jan 27, 2022)
10-35607869-C-T		not specified	Uncertain significance (Oct 26, 2022)
10-35607904-C-A		not specified	Uncertain significance (Nov 21, 2023)
10-35607922-C-T		not specified	Uncertain significance (Oct 30, 2024)
10-35607961-C-T		not specified	Uncertain significance (Apr 12, 2024)
10-35607985-G-C		not specified	Uncertain significance (Feb 16, 2023)
10-35608040-C-G		not specified	Uncertain significance (Mar 07, 2023)
10-35608057-G-C		not specified	Uncertain significance (Feb 17, 2024)
10-35608060-G-A		not specified	Uncertain significance (Aug 30, 2021)
10-35608097-C-T		not specified	Uncertain significance (Dec 05, 2024)
10-35608120-G-T		not specified	Uncertain significance (Jun 13, 2024)
10-35608157-A-G		not specified	Uncertain significance (Sep 22, 2022)
10-35608174-C-T		not specified	Uncertain significance (Jul 12, 2022)
10-35608184-T-G		not specified	Uncertain significance (May 24, 2023)
10-35608196-C-G		not specified	Uncertain significance (Dec 10, 2024)
10-35608196-C-T		not specified	Uncertain significance (Aug 01, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
GJD4	protein_coding	protein_coding	ENST00000321660	2	3526

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0150	0.469	125556	0	148	125704	0.000589

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-1.01	266	224	1.19	0.0000149	2264
Missense in 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

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000904	0.0000904
Ashkenazi Jewish	0.00	0.00
East Asian	0.00707	0.00709
Finnish	0.00	0.00
European (Non-Finnish)	0.00	0.00
Middle Eastern	0.00707	0.00709
South Asian	0.000490	0.000490
Other	0.000163	0.000163

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}.

Recessive Scores

• pRec: 0.0994

Haploinsufficiency Scores

• pHI: 0.106
• hipred: N
• hipred_score: 0.180
• ghis: 0.421

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.0151

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Gjd4
• Phenotype: immune system phenotype; hematopoietic system phenotype; muscle phenotype

Gene ontology

• Biological process: cell communication;regulation of satellite cell activation involved in skeletal muscle regeneration
• Cellular component: connexin complex;integral component of membrane