GJA9

protein-coding

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

Gene summary

Connexins, such as GJA9, are involved in the formation of gap junctions, intercellular conduits that directly connect the cytoplasms of contacting cells. Each gap junction channel is formed by docking of 2 hemichannels, each of which contains 6 connexin subunits (Sohl et al., 2003 [PubMed 12881038]).[supplied by OMIM, Mar 2008]

Previous symbols:

GJA10

MANE transcript

NM_030772.5

Inheritance

—

ClinVar variants

U:68B:4

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 1.05

Max pathogenic AF

—

Genomic locus

chr1:38,874,069-38,881,587

External References & Databases

Ensembl (ENSG00000131233)

Transcript & Mutation Effects

hg38 • Region Span ~7.5 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to GJA9 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 67

not providedTotal: 3

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_030772.5. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous				1 clinvar		1
missense			66 clinvar	1 clinvar	2 clinvar	69
nonsense						0
start loss						0
frameshift			2 clinvar			2
splice donor/acceptor (+/-2bp)						0
Total	0	0	68	2	2	72

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 3 of 3 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_030772.5	RefSeq	NP_110399.2	1	MANE Select
ENST00000357771.5	Ensembl	ENSP00000350415.3	1	MANE Select
ENST00000360786.3	Ensembl	ENSP00000354020.3	1	Standard

Model Organisms & Knockout Phenotypes

Observed phenotypic effects in mouse and zebrafish models

Gene / Model	Organism	Observed Phenotype
cx55.5	Danio rerio	Structure: horizontal cell Quality: functionality abnormal

Gene / Model

Organism

Observed Phenotype

cx55.5

Danio rerio

Structure: horizontal cell

Quality: functionality

abnormal

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

Calcium Regulation in the Cardiac Cell

Biological Process

cell communication

Cellular Component

connexin complex
integral component of membrane

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000357771
Coding exons: 1
Length: 17115
Individuals with no LoFs: 125657
Homozygous LoFs: 0
Heterozygous LoFs: 90
Defined: 125747
p: 0.000358

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.935	222	265	0.838	0.0000134	3387
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00025	0.00025	rare
Latino/Admixed American	0.00046	0.00046	rare
Ashkenazi Jewish	0.000099	0.000099	rare
East Asian	0.00027	0.00027	rare
Finnish	0.000092	0.000092	rare
European (Non-Finnish)	0.00035	0.00035	rare
South Asian	0.00059	0.00059	rare
Other	0.00065	0.00065	rare

dbNSFP Gene Annotations

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}.;

Recessive Scores

pRec: 0.124

Intolerance Scores

LoFtool: 0.365
RVIS EVS: 0.95
RVIS percentile EVS: 90.06

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Indispensability pred.: N
Indispensability score: 0.0528

Gene Damage Prediction

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