GJD2

gap junction protein delta 2, the group of Gap junction proteins

Basic information

Region (hg38): 15:34751032-34754998

Previous symbols: [ "GJA9" ]

Links

ENSG00000159248

∙ NCBI:57369 ∙ OMIM:607058 ∙ HGNC:19154 ∙ Uniprot:Q9UKL4 ∙ 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 GJD2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the GJD2 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			13 clinvar		1 clinvar	14
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	13	0	1

Variants in GJD2

This is a list of pathogenic ClinVar variants found in the GJD2 region.

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

Position	Phenotype	Significance	ClinVar
15-34752594-C-T	not specified	Uncertain significance (Oct 06, 2024)	3520333
15-34752597-C-A	not specified	Uncertain significance (Jun 18, 2024)	3281470
15-34752612-G-A	not specified	Uncertain significance (Jan 26, 2022)	2273358
15-34752891-A-T	not specified	Uncertain significance (Sep 30, 2024)	2365246
15-34752912-G-A	not specified	Uncertain significance (Dec 16, 2022)	2336169
15-34752933-C-T	not specified	Uncertain significance (Sep 26, 2022)	2235924
15-34752962-C-T	not specified	Uncertain significance (Dec 12, 2023)	3100003
15-34752980-T-G	not specified	Uncertain significance (Dec 07, 2024)	3520331
15-34752986-A-G	not specified	Uncertain significance (May 23, 2024)	3281469
15-34753043-C-T	not specified	Uncertain significance (Dec 05, 2022)	2332707
15-34753049-C-G		Benign (Jun 18, 2018)	715052
15-34753091-C-T	not specified	Uncertain significance (Jan 02, 2024)	3100002
15-34753105-G-T	not specified	Uncertain significance (Jun 21, 2022)	2295664
15-34753121-C-T	not specified	Uncertain significance (Oct 01, 2024)	2282169
15-34753124-C-T	not specified	Uncertain significance (Sep 22, 2022)	2219486
15-34753140-C-A	not specified	Uncertain significance (Jan 08, 2024)	3100001
15-34753229-G-T	not specified	Uncertain significance (Oct 17, 2023)	3100000
15-34753305-C-T	not specified	Uncertain significance (Jul 17, 2023)	2598979
15-34753334-A-G	not specified	Uncertain significance (Nov 08, 2024)	3520332

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
GJD2	protein_coding	protein_coding	ENST00000290374	2	3934

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.197	0.794	125742	0	6	125748	0.0000239

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.43	91	184	0.495	0.0000104	2081
Missense in Polyphen		26	80.085	0.32466		883
Synonymous	-0.808	78	69.4	1.12	0.00000326	669
Loss of Function	2.24	3	11.1	0.272	7.43e-7	124

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000124	0.000123
Ashkenazi Jewish	0.0000992	0.0000992
East Asian	0.00	0.00
Finnish	0.0000924	0.0000924
European (Non-Finnish)	0.00000879	0.00000879
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.;
Pathway: Gap junction - Homo sapiens (human);Calcium Regulation in the Cardiac Cell;Electric Transmission Across Gap Junctions;Transmission across Electrical Synapses ;Neuronal System (Consensus)

Recessive Scores

pRec: 0.194

Intolerance Scores

loftool: 0.179
rvis_EVS: -0.27
rvis_percentile_EVS: 34.32

Haploinsufficiency Scores

pHI: 0.333
hipred: Y
hipred_score: 0.736
ghis: 0.566

Essentials

essential_gene_CRISPR: N
essential_gene_CRISPR2: S
essential_gene_gene_trap: N
gene_indispensability_pred: N
gene_indispensability_score: 0.459

Gene Damage Prediction

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

Mouse Genome Informatics

Gene name: Gjd2
Phenotype: endocrine/exocrine gland phenotype; homeostasis/metabolism phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); vision/eye phenotype; nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan);

Zebrafish Information Network

Gene name: gjd2a
Affected structure: afferent neuron
Phenotype tag: abnormal
Phenotype quality: absent

Gene ontology

Biological process: action potential;chemical synaptic transmission;visual perception;transmembrane transport
Cellular component: plasma membrane;connexin complex;integral component of membrane
Molecular function: gap junction channel activity