ASIC1

acid sensing ion channel subunit 1, the group of Acid sensing ion channel subunits

Basic information

Region (hg38): 12:50057547-50083611

Previous symbols: [ "ACCN2" ]

Links

ENSG00000110881 ∙ NCBI:41 ∙ OMIM:602866 ∙ HGNC:100 ∙ Uniprot:P78348 ∙ 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 ASIC1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ASIC1 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	2	3
missense			21		1	22
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)			1			1
splice region					1	1
non coding					1	1
Total	0	0	22	1	4

Variants in ASIC1

This is a list of pathogenic ClinVar variants found in the ASIC1 region.

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

Position	Type	Phenotype	Significance	ClinVar
12-50058782-G-C		not specified	Uncertain significance (Nov 17, 2023)
12-50058810-C-G		not specified	Uncertain significance (Dec 02, 2022)
12-50058822-A-C		not specified	Uncertain significance (Apr 27, 2023)
12-50058844-A-G			Benign (Apr 24, 2018)
12-50059095-A-C		not specified	Uncertain significance (Jun 25, 2022)
12-50059122-A-G		not specified	Uncertain significance (Jan 27, 2022)
12-50059757-A-G		Seizure	Uncertain significance (Jan 01, 2019)
12-50059893-G-A		not specified	Uncertain significance (May 05, 2023)
12-50059957-G-A			Benign (Jun 11, 2018)
12-50077295-C-T		not specified	Uncertain significance (Dec 28, 2022)
12-50077326-C-T			Benign (Jul 16, 2018)
12-50078126-G-A		not specified	Uncertain significance (Nov 05, 2021)
12-50078520-G-A		not specified	Uncertain significance (Sep 28, 2022)
12-50078530-C-T		not specified	Uncertain significance (Feb 13, 2024)
12-50078559-C-T		not specified	Uncertain significance (Oct 06, 2021)
12-50080015-T-C		not specified	Uncertain significance (Dec 21, 2022)
12-50080489-C-T			Benign (Apr 24, 2018)
12-50080622-T-C		not specified	Uncertain significance (Mar 01, 2023)
12-50080626-A-G			Benign (Jul 10, 2018)
12-50080634-G-A		not specified	Uncertain significance (Sep 17, 2021)
12-50080636-C-T		not specified	Likely benign (Dec 13, 2023)
12-50080637-G-T		not specified	Uncertain significance (Sep 13, 2023)
12-50081292-A-C		not specified	Uncertain significance (May 18, 2023)
12-50081295-C-G		not specified	Uncertain significance (Aug 21, 2023)
12-50081330-G-A			Uncertain significance (Jan 01, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ASIC1	protein_coding	protein_coding	ENST00000228468	11	26064

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.930	0.0698	125730	0	12	125742	0.0000477

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.82	207	357	0.580	0.0000216	3760
Missense in Polyphen		41	106.02	0.38672		1102
Synonymous	0.579	140	149	0.940	0.00000979	1098
Loss of Function	4.28	5	30.5	0.164	0.00000173	316

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.000232	0.000231
European (Non-Finnish)	0.0000531	0.0000527
Middle Eastern	0.00	0.00
South Asian	0.0000327	0.0000327
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Isoform 2 and isoform 3 function as proton-gated sodium channels; they are activated by a drop of the extracellular pH and then become rapidly desensitized. The channel generates a biphasic current with a fast inactivating and a slow sustained phase. Has high selectivity for sodium ions and can also transport lithium ions with high efficiency. Isoform 2 can also transport potassium, but with lower efficiency. It is nearly impermeable to the larger rubidium and cesium ions. Isoform 3 can also transport calcium ions. Mediates glutamate-independent Ca(2+) entry into neurons upon acidosis. This Ca(2+) overloading is toxic for cortical neurons and may be in part responsible for ischemic brain injury. Heteromeric channel assembly seems to modulate channel properties. Functions as a postsynaptic proton receptor that influences intracellular Ca(2+) concentration and calmodulin-dependent protein kinase II phosphorylation and thereby the density of dendritic spines. Modulates activity in the circuits underlying innate fear. {ECO:0000269|PubMed:22760635}.
• Pathway: Inflammatory mediator regulation of TRP channels - Homo sapiens (human);Stimuli-sensing channels;Ion channel transport;Transport of small molecules (Consensus)

Recessive Scores

• pRec: 0.175

Intolerance Scores

• rvis_EVS: -0.49
• rvis_percentile_EVS: 22.36

Haploinsufficiency Scores

• pHI: 0.237
• hipred: Y
• hipred_score: 0.725
• ghis: 0.645

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.114

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Asic1
• 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); behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan)

Gene ontology

• Biological process: behavioral fear response;response to amphetamine;sodium ion transport;signal transduction;memory;associative learning;response to pH;response to acidic pH;ion transmembrane transport;sodium ion transmembrane transport;regulation of membrane potential;negative regulation of neurotransmitter secretion;sensory perception of sour taste;protein homotrimerization;calcium ion transmembrane transport;cellular response to pH
• Cellular component: Golgi apparatus;plasma membrane;integral component of plasma membrane;cell surface;synapse
• Molecular function: protein binding;ligand-gated sodium channel activity;acid-sensing ion channel activity