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.

not_specified (25 variants)
not_provided (1 variants)

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. These statistics are base on transcript: NM_000020660.3. Only rare variants are included in the table.

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.

Effect	PathogenicP	Likely pathogenicLP	VUSVUS	Likely benignLB	BenignB	Sum
synonymous						0
missense			25 clinvar		1 clinvar	26
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	25	0	1

Loading clinvar variants...

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