GJB5

gap junction protein beta 5, the group of Gap junction proteins

Basic information

Region (hg38): 1:34755047-34758512

Links

ENSG00000189280 ∙ NCBI:2709 ∙ OMIM:604493 ∙ HGNC:4287 ∙ Uniprot:O95377 ∙ 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 GJB5 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the GJB5 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			18	2		20
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	18	2	0

Variants in GJB5

This is a list of pathogenic ClinVar variants found in the GJB5 region.

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

Position	Type	Phenotype	Significance	ClinVar
1-34757356-T-C		not specified	Uncertain significance (Jul 06, 2021)
1-34757394-C-T		not specified	Uncertain significance (Aug 30, 2021)
1-34757413-T-C		not specified	Uncertain significance (Dec 14, 2023)
1-34757418-A-G		not specified	Uncertain significance (Apr 04, 2023)
1-34757455-G-A		not specified	Uncertain significance (Apr 07, 2022)
1-34757529-G-A		not specified	Uncertain significance (Nov 30, 2021)
1-34757554-G-A		not specified	Uncertain significance (Aug 12, 2021)
1-34757622-C-T		not specified	Uncertain significance (Jan 18, 2022)
1-34757640-A-G		not specified	Uncertain significance (Jun 29, 2023)
1-34757692-G-T		not specified	Uncertain significance (Feb 15, 2023)
1-34757695-A-G		not specified	Uncertain significance (Feb 22, 2023)
1-34757700-C-T		not specified	Uncertain significance (Mar 20, 2024)
1-34757750-C-A		not specified	Uncertain significance (Jun 10, 2022)
1-34757751-G-A		not specified	Uncertain significance (Jul 29, 2022)
1-34757821-G-A		not specified	Uncertain significance (Jun 23, 2023)
1-34757842-A-G		not specified	Uncertain significance (Apr 25, 2022)
1-34757878-A-G		not specified	Uncertain significance (Jul 26, 2022)
1-34757893-T-G		not specified	Uncertain significance (Apr 19, 2024)
1-34757916-A-G		not specified	Likely benign (Feb 05, 2024)
1-34757937-G-A		not specified	Uncertain significance (May 15, 2024)
1-34758004-T-C		not specified	Likely benign (Apr 04, 2024)
1-34758097-A-G		not specified	Uncertain significance (Feb 15, 2023)
1-34758117-C-T		not specified	Uncertain significance (Apr 20, 2023)
1-34758118-G-A		not specified	Likely benign (Aug 23, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
GJB5	protein_coding	protein_coding	ENST00000338513	1	3466

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0000137	0.237	125697	0	51	125748	0.000203

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.0493	164	166	0.989	0.0000105	1791
Missense in Polyphen		68	64.863	1.0484		778
Synonymous	-0.210	71	68.8	1.03	0.00000450	560
Loss of Function	-0.248	7	6.33	1.11	3.61e-7	67

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000445	0.000445
Ashkenazi Jewish	0.00	0.00
East Asian	0.000761	0.000761
Finnish	0.00	0.00
European (Non-Finnish)	0.000185	0.000185
Middle Eastern	0.000761	0.000761
South Asian	0.000131	0.000131
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: Calcium Regulation in the Cardiac Cell (Consensus)

Recessive Scores

• pRec: 0.133

Intolerance Scores

• loftool: 0.322
• rvis_EVS: -0.05
• rvis_percentile_EVS: 50.22

Haploinsufficiency Scores

• pHI: 0.182
• hipred: N
• hipred_score: 0.248
• ghis: 0.553

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.222

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Gjb5
• 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); embryo phenotype; growth/size/body region phenotype

Gene ontology

• Biological process: cell communication;epidermis development;trophoblast giant cell differentiation;spongiotrophoblast differentiation;labyrinthine layer morphogenesis;epididymis development
• Cellular component: connexin complex;integral component of membrane