GJA4

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

Basic information

Region (hg38): 1:34792999-34795747

Links

ENSG00000187513 ∙ NCBI:2701 ∙ OMIM:121012 ∙ HGNC:4278 ∙ Uniprot:P35212 ∙ 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 GJA4 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the GJA4 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						0
missense			19	1	2	22
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	19	1	2

Variants in GJA4

This is a list of pathogenic ClinVar variants found in the GJA4 region.

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

Position	Type	Phenotype	Significance	ClinVar
1-34794266-C-T		not specified	Uncertain significance (Nov 17, 2022)
1-34794271-G-A		not specified	Uncertain significance (Jul 30, 2024)
1-34794295-G-A		not specified	Uncertain significance (Jun 07, 2024)
1-34794295-G-T		not specified	Uncertain significance (Dec 28, 2023)
1-34794334-G-T		Cutaneous venous malformation • Hepatic hemangioma • Skin hemangioma	Pathogenic (Apr 08, 2021)
1-34794442-T-C		not specified	Uncertain significance (Mar 20, 2024)
1-34794461-T-C		not specified	Uncertain significance (Aug 09, 2021)
1-34794467-T-A		not specified	Uncertain significance (Sep 18, 2024)
1-34794560-T-G		not specified	Uncertain significance (Aug 15, 2023)
1-34794571-G-T		not specified	Uncertain significance (Nov 13, 2024)
1-34794587-G-A		not specified	Uncertain significance (Mar 25, 2024)
1-34794599-C-A		not specified	Uncertain significance (Dec 07, 2021)
1-34794607-C-T			Benign (Feb 01, 2023)
1-34794632-C-T		not specified	Uncertain significance (Aug 19, 2023)
1-34794652-A-G		not specified	Uncertain significance (Jul 20, 2022)
1-34794654-C-G		not specified	Uncertain significance (Jan 24, 2024)
1-34794682-G-A			Uncertain significance (Jan 23, 2024)
1-34794745-G-A		not specified	Uncertain significance (Feb 28, 2023)
1-34794763-G-A		not specified	Uncertain significance (Feb 15, 2023)
1-34794781-G-A		not specified	Uncertain significance (Dec 09, 2024)
1-34794818-G-A		not specified	Uncertain significance (Jan 31, 2022)
1-34794824-C-T		not specified	Uncertain significance (Nov 17, 2022)
1-34794836-T-C			Uncertain significance (Sep 24, 2024)
1-34794905-T-C		not specified	Uncertain significance (Aug 29, 2024)
1-34794911-G-A		not specified	Uncertain significance (Dec 11, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
GJA4	protein_coding	protein_coding	ENST00000342280	1	2750

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0558	0.927	125712	0	35	125747	0.000139

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.21	166	216	0.768	0.0000143	2108
Missense in Polyphen		48	81.264	0.59067		872
Synonymous	0.830	84	94.2	0.891	0.00000617	725
Loss of Function	2.08	4	11.7	0.343	6.71e-7	107

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000362	0.000362
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000544	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.0000529	0.0000527
Middle Eastern	0.0000544	0.0000544
South Asian	0.000653	0.000653
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.
• Pathway: Ovarian Infertility Genes;Calcium Regulation in the Cardiac Cell (Consensus)

Intolerance Scores

• loftool: 0.184
• rvis_EVS: 0.4
• rvis_percentile_EVS: 76.31

Haploinsufficiency Scores

• pHI: 0.164
• hipred: N
• hipred_score: 0.465
• ghis: 0.456

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.155

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Gja4
• Phenotype: digestive/alimentary phenotype; respiratory system phenotype; mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); reproductive system 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); endocrine/exocrine gland phenotype; muscle phenotype

Zebrafish Information Network

• Gene name: cx39.4
• Affected structure: iridophore
• Phenotype tag: abnormal
• Phenotype quality: dispersed

Gene ontology

• Biological process: blood vessel development;endothelium development;calcium ion transport;cell-cell junction assembly;cell-cell signaling;response to pain
• Cellular component: integral component of plasma membrane;gap junction;connexin complex
• Molecular function: protein binding