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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

ENSG00000110881NCBI:41OMIM:602866HGNC:100Uniprot:P78348AlphaFoldGenCCjaxSfariGnomADPubmedClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the ASIC1 gene.

  • Inborn genetic diseases (16 variants)
  • not provided (5 variants)
  • Seizure (1 variants)

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
2
clinvar
2
missense
16
clinvar
1
clinvar
17
nonsense
0
start loss
0
frameshift
0
inframe indel
0
splice donor/acceptor (+/-2bp)
1
clinvar
1
splice region
1
1
non coding
1
clinvar
1
Total 0 0 17 0 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
12-50058810-C-G Inborn genetic diseases Uncertain significance (Dec 02, 2022)2332095
12-50058822-A-C Inborn genetic diseases Uncertain significance (Apr 27, 2023)2516694
12-50058844-A-G Benign (Apr 24, 2018)714537
12-50059095-A-C Inborn genetic diseases Uncertain significance (Jun 25, 2022)2297646
12-50059122-A-G Inborn genetic diseases Uncertain significance (Jan 27, 2022)2274089
12-50059757-A-G Seizure Uncertain significance (Jan 01, 2019)982934
12-50059893-G-A Inborn genetic diseases Uncertain significance (May 05, 2023)2514744
12-50059957-G-A Benign (Jun 11, 2018)719748
12-50077295-C-T Inborn genetic diseases Uncertain significance (Dec 28, 2022)2394787
12-50077326-C-T Benign (Jul 16, 2018)783660
12-50078126-G-A Inborn genetic diseases Uncertain significance (Nov 05, 2021)2258991
12-50078559-C-T Inborn genetic diseases Uncertain significance (Oct 06, 2021)2253704
12-50080015-T-C Inborn genetic diseases Uncertain significance (Dec 21, 2022)2338627
12-50080489-C-T Benign (Apr 24, 2018)784239
12-50080622-T-C Inborn genetic diseases Uncertain significance (Mar 01, 2023)2492028
12-50080626-A-G Benign (Jul 10, 2018)779524
12-50080634-G-A Inborn genetic diseases Uncertain significance (Sep 17, 2021)2206977
12-50080637-G-T Inborn genetic diseases Uncertain significance (Sep 13, 2023)2589037
12-50081292-A-C Inborn genetic diseases Uncertain significance (May 18, 2023)2525676
12-50081295-C-G Inborn genetic diseases Uncertain significance (Aug 21, 2023)2620114
12-50081330-G-A Uncertain significance (Jan 01, 2024)3027077
12-50081353-G-A Inborn genetic diseases Uncertain significance (Aug 02, 2021)2403082
12-50081564-G-A Inborn genetic diseases Uncertain significance (Aug 14, 2023)2618235

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
ASIC1protein_codingprotein_codingENST00000228468 1126064
pLI Probability
LOF Intolerant
pRec Probability
LOF Recessive
Individuals with
no LOFs
Individuals with
Homozygous LOFs
Individuals with
Heterozygous LOFs
Defined p
0.9300.06981257300121257420.0000477
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense2.822073570.5800.00002163760
Missense in Polyphen41106.020.386721102
Synonymous0.5791401490.9400.000009791098
Loss of Function4.28530.50.1640.00000173316

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.000.00
Ashkenazi Jewish0.000.00
East Asian0.000.00
Finnish0.0002320.000231
European (Non-Finnish)0.00005310.0000527
Middle Eastern0.000.00
South Asian0.00003270.0000327
Other0.000.00

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

loftool
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

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium

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