PANX1

pannexin 1, the group of Pannexins

Basic information

Region (hg38): 11:94128840-94181968

Links

ENSG00000110218 ∙ NCBI:24145 ∙ OMIM:608420 ∙ HGNC:8599 ∙ Uniprot:Q96RD7 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• oocyte maturation defect 7 (Strong), mode of inheritance: AD

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Oocyte/zygote/embryo maturation arrest 7	AD	General	Genetic knowledge may be beneficial related to issues such as selection of optimal supportive care, informed medical decision-making, prognostic considerations, and avoidance of unnecessary testing	Obstetric	30918116

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the PANX1 gene.

• not provided (22 variants)
• Inborn genetic diseases (17 variants)
• Oocyte maturation defect 7 (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PANX1 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	2
missense			15	5	4	24
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding				1	12	13
Total	0	0	15	7	17

Variants in PANX1

This is a list of pathogenic ClinVar variants found in the PANX1 region.

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

Position	Type	Phenotype	Significance	ClinVar
11-94128854-C-T			Benign (Jun 19, 2021)
11-94129088-TCCCGC-T			Benign (Jun 21, 2021)
11-94129292-C-G			Benign (Jun 20, 2021)
11-94129327-A-C		Oocyte maturation defect 7	Benign (Sep 05, 2021)
11-94129334-A-G		not specified	Uncertain significance (Apr 18, 2023)
11-94129361-C-G		not specified	Uncertain significance (Dec 09, 2023)
11-94129365-AGGAGCCCAC-A		Oocyte maturation defect 7	Pathogenic (Apr 10, 2023)
11-94129380-C-G		not specified	Uncertain significance (Nov 20, 2023)
11-94129393-G-T			Benign (Dec 31, 2019)
11-94129411-T-C			Likely benign (Feb 09, 2018)
11-94153499-A-G		not specified	Uncertain significance (Feb 05, 2024)
11-94153500-T-C		not specified	Uncertain significance (Aug 19, 2023)
11-94153570-T-C		PANX1-related disorder	Likely benign (May 28, 2019)
11-94153571-G-T		not specified	Uncertain significance (Jun 09, 2022)
11-94153609-C-A		not specified	Uncertain significance (Dec 26, 2023)
11-94153672-G-C			Benign (Jun 19, 2021)
11-94178421-T-C		not specified	Uncertain significance (Sep 16, 2021)
11-94178429-C-T		not specified	Uncertain significance (Sep 12, 2023)
11-94178430-G-A		not specified	Uncertain significance (Jul 06, 2021)
11-94178435-G-A		not specified	Likely benign (Aug 22, 2023)
11-94178502-G-A		not specified	Uncertain significance (Feb 12, 2024)
11-94178512-G-C			Likely benign (Dec 31, 2019)
11-94178519-A-G		not specified	Uncertain significance (Dec 20, 2023)
11-94178526-C-T		not specified	Likely benign (Apr 25, 2022)
11-94178566-A-G		PANX1-related disorder	Likely benign (Sep 10, 2019)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PANX1	protein_coding	protein_coding	ENST00000227638	5	53045

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00000247	0.751	125709	0	39	125748	0.000155

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.424	255	237	1.08	0.0000126	2783
Missense in Polyphen		98	99.65	0.98344		1154
Synonymous	-0.330	107	103	1.04	0.00000613	842
Loss of Function	1.22	11	16.3	0.675	7.74e-7	197

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000177	0.000177
Ashkenazi Jewish	0.00	0.00
East Asian	0.000163	0.000163
Finnish	0.00	0.00
European (Non-Finnish)	0.000160	0.000158
Middle Eastern	0.000163	0.000163
South Asian	0.000414	0.000392
Other	0.000172	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Structural component of the gap junctions and the hemichannels. May play a role as a Ca(2+)-leak channel to regulate ER Ca(2+) homeostasis. {ECO:0000269|PubMed:16908669, ECO:0000269|PubMed:20829356}.
• Pathway: NOD-like receptor signaling pathway - Homo sapiens (human);miR-targeted genes in lymphocytes - TarBase;miR-targeted genes in muscle cell - TarBase;Electric Transmission Across Gap Junctions;Transmission across Electrical Synapses ;Neuronal System (Consensus)

Recessive Scores

• pRec: 0.111

Intolerance Scores

• loftool: 0.570
• rvis_EVS: 0.35
• rvis_percentile_EVS: 74.49

Haploinsufficiency Scores

• pHI: 0.116
• hipred: N
• hipred_score: 0.319
• ghis: 0.424

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.282

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Panx1
• Phenotype: homeostasis/metabolism phenotype; cellular 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; immune system phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); respiratory system phenotype; hematopoietic system phenotype

Zebrafish Information Network

• Gene name: panx1a
• Affected structure: brain
• Phenotype tag: abnormal
• Phenotype quality: decreased amount

Gene ontology

• Biological process: response to ischemia;cation transport;calcium ion transport;cell-cell signaling;response to ATP;protein hexamerization;positive regulation of interleukin-1 alpha secretion;positive regulation of interleukin-1 beta secretion;calcium ion transmembrane transport
• Cellular component: endoplasmic reticulum;endoplasmic reticulum membrane;plasma membrane;gap junction;membrane;integral component of membrane;bleb;protein-containing complex
• Molecular function: protease binding;signaling receptor binding;calcium channel activity;wide pore channel activity;leak channel activity;ion channel binding;protein heterodimerization activity;actin filament binding;gap junction hemi-channel activity;scaffold protein binding