GJA9

gap junction protein alpha 9, the group of Gap junction proteins

Basic information

Region (hg38): 1:38874069-38881587

Previous symbols: [ "GJA10" ]

Links

ENSG00000131233 ∙ NCBI:81025 ∙ OMIM:611923 ∙ HGNC:19155 ∙ Uniprot:P57773 ∙ 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 GJA9 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the GJA9 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			39		2	41
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	39	1	2

Variants in GJA9

This is a list of pathogenic ClinVar variants found in the GJA9 region.

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

Position	Type	Phenotype	Significance	ClinVar
1-38874559-G-C		not specified	Uncertain significance (Feb 28, 2024)
1-38874586-T-G		not specified	Uncertain significance (Mar 14, 2023)
1-38874597-G-A		not specified	Uncertain significance (Sep 17, 2021)
1-38874709-A-G			Benign (Jun 19, 2018)
1-38874747-G-A			Benign (Jun 19, 2018)
1-38874751-C-T		not specified	Uncertain significance (May 10, 2022)
1-38874853-C-G		not specified	Uncertain significance (Dec 22, 2023)
1-38874932-A-G			Likely benign (Sep 10, 2018)
1-38874936-C-T		not specified	Uncertain significance (May 04, 2022)
1-38874971-T-G		not specified	Uncertain significance (Feb 25, 2025)
1-38874993-T-A		not specified	Uncertain significance (Mar 06, 2025)
1-38874995-C-A		not specified	Uncertain significance (Mar 06, 2025)
1-38875000-A-C		not specified	Uncertain significance (Sep 03, 2024)
1-38875003-G-T		not specified	Uncertain significance (Oct 12, 2024)
1-38875089-C-T		not specified	Uncertain significance (Aug 23, 2021)
1-38875123-C-G		not specified	Uncertain significance (Dec 06, 2022)
1-38875157-A-T		not specified	Uncertain significance (Jun 07, 2023)
1-38875158-C-G		not specified	Uncertain significance (Apr 22, 2022)
1-38875173-T-G		not specified	Uncertain significance (Jan 03, 2024)
1-38875206-G-A		not specified	Uncertain significance (Jul 30, 2024)
1-38875210-A-T		not specified	Uncertain significance (Dec 20, 2023)
1-38875237-C-G		not specified	Uncertain significance (Jul 29, 2023)
1-38875263-G-A		not specified	Uncertain significance (Jul 17, 2024)
1-38875308-A-T		not specified	Uncertain significance (Nov 09, 2024)
1-38875329-G-A		not specified	Uncertain significance (Feb 28, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
GJA9	protein_coding	protein_coding	ENST00000357771	1	17115

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
4.65e-12	0.0284	125657	0	90	125747	0.000358

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.935	222	265	0.838	0.0000134	3387
Missense in Polyphen		52	59.421	0.87511		794
Synonymous	1.03	87	100	0.869	0.00000505	1011
Loss of Function	-0.169	17	16.3	1.05	9.34e-7	194

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000709	0.000709
Ashkenazi Jewish	0.0000992	0.0000992
East Asian	0.000272	0.000272
Finnish	0.0000924	0.0000924
European (Non-Finnish)	0.000352	0.000352
Middle Eastern	0.000272	0.000272
South Asian	0.000589	0.000588
Other	0.000653	0.000652

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}.
• Pathway: Calcium Regulation in the Cardiac Cell (Consensus)

Recessive Scores

• pRec: 0.124

Intolerance Scores

• loftool: 0.365
• rvis_EVS: 0.95
• rvis_percentile_EVS: 90.06

Haploinsufficiency Scores

• pHI: 0.597
• hipred: N
• hipred_score: 0.170

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.0528

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Gja10
• 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); vision/eye phenotype

Zebrafish Information Network

• Gene name: cx55.5
• Affected structure: horizontal cell
• Phenotype tag: abnormal
• Phenotype quality: functionality

Gene ontology

• Biological process: cell communication
• Cellular component: connexin complex;integral component of membrane