CALHM1
Basic information
Region (hg38): 10:103453240-103458900
Previous symbols: [ "FAM26C" ]
Links
Phenotypes
GenCC
Source:
ClinVar
This is a list of variants' phenotypes submitted to
- not_specified (61 variants)
- not_provided (3 variants)
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the CALHM1 gene is commonly pathogenic or not. These statistics are base on transcript: NM_001001412.4. Only rare variants are included in the table.
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.
| Effect | PathogenicP | Likely pathogenicLP | VUSVUS | Likely benignLB | BenignB | Sum |
|---|---|---|---|---|---|---|
| synonymous | 0 | |||||
| missense | 62 | 64 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| Total | 0 | 1 | 62 | 0 | 1 |
Highest pathogenic variant AF is 0.0000707223
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| CALHM1 | protein_coding | protein_coding | ENST00000329905 | 2 | 5502 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.0000176 | 0.459 | 125483 | 1 | 246 | 125730 | 0.000983 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | -0.166 | 255 | 248 | 1.03 | 0.0000176 | 2224 |
| Missense in Polyphen | 97 | 99.816 | 0.97179 | 1023 | ||
| Synonymous | -0.737 | 127 | 117 | 1.09 | 0.00000925 | 751 |
| Loss of Function | 0.487 | 8 | 9.63 | 0.831 | 4.99e-7 | 97 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.000773 | 0.000760 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.000163 | 0.000163 |
| Finnish | 0.00477 | 0.00477 |
| European (Non-Finnish) | 0.000207 | 0.000185 |
| Middle Eastern | 0.000163 | 0.000163 |
| South Asian | 0.00329 | 0.00327 |
| Other | 0.000823 | 0.000815 |
dbNSFP
Source:
- Function
- FUNCTION: Pore-forming subunit of a voltage-gated ion channel required for sensory perception of sweet, bitter and umami tastes. Specifically present in type II taste bud cells, where it plays a central role in sweet, bitter and umami taste perception by inducing ATP release from the cell, ATP acting as a neurotransmitter to activate afferent neural gustatory pathways. Acts both as a voltage-gated and calcium-activated ion channel: mediates neuronal excitability in response to changes in extracellular Ca(2+) concentration. Has poor ion selectivity and forms a wide pore (around 14 Angstroms) that mediates permeation of Ca(2+), Na(+) and K(+), as well as permeation of monovalent anions. Acts as an activator of the ERK1 and ERK2 cascade. Triggers endoplasmic reticulum stress by reducing the calcium content of the endoplasmic reticulum. May indirectly control amyloid precursor protein (APP) proteolysis and aggregated amyloid-beta (Abeta) peptides levels in a Ca(2+) dependent manner. {ECO:0000269|PubMed:18585350, ECO:0000269|PubMed:21574960, ECO:0000269|PubMed:22711817, ECO:0000269|PubMed:23300080, ECO:0000269|PubMed:23345406}.;
- Pathway
- Taste transduction - Homo sapiens (human)
(Consensus)
Recessive Scores
- pRec
- 0.110
Intolerance Scores
- loftool
- 0.659
- rvis_EVS
- -0.11
- rvis_percentile_EVS
- 45.57
Haploinsufficiency Scores
- pHI
- 0.207
- hipred
- N
- hipred_score
- 0.350
- ghis
- 0.411
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- N
- gene_indispensability_score
- 0.205
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Calhm1
- 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); homeostasis/metabolism phenotype;
Gene ontology
- Biological process
- cation transport;ATP transport;regulation of ion transmembrane transport;sensory perception of bitter taste;sensory perception of sweet taste;sensory perception of umami taste;protein homooligomerization;calcium ion transmembrane transport
- Cellular component
- endoplasmic reticulum membrane;integral component of plasma membrane
- Molecular function
- calcium activated cation channel activity;voltage-gated ion channel activity;voltage-gated calcium channel activity;identical protein binding