CALHM1

calcium homeostasis modulator 1, the group of Calcium homeostasis modulators

Basic information

Region (hg38): 10:103453239-103458900

Previous symbols: [ "FAM26C" ]

Links

ENSG00000185933 ∙ NCBI:255022 ∙ OMIM:612234 ∙ HGNC:23494 ∙ Uniprot:Q8IU99 ∙ 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 CALHM1 gene.

• Inborn genetic diseases (17 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.

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						0
missense		1	18		1	20
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	1	18	0	1

Highest pathogenic variant AF is 0.0000460

Variants in CALHM1

This is a list of pathogenic ClinVar variants found in the CALHM1 region.

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

Position	Type	Phenotype	Significance	ClinVar
10-103455291-C-T		not specified	Uncertain significance (Dec 16, 2023)
10-103455321-C-A		not specified	Uncertain significance (May 09, 2023)
10-103455327-C-T		not specified	Uncertain significance (Aug 09, 2021)
10-103455342-G-T		not specified	Uncertain significance (Feb 27, 2023)
10-103455348-C-T		not specified	Uncertain significance (Nov 18, 2022)
10-103455371-G-A		not specified	Uncertain significance (May 26, 2022)
10-103455414-C-A		not specified	Uncertain significance (Jan 24, 2024)
10-103455432-G-A		not specified	Uncertain significance (Oct 12, 2021)
10-103455455-G-A		not specified	Uncertain significance (Jun 24, 2022)
10-103455489-C-T		not specified	Uncertain significance (Nov 18, 2022)
10-103455602-G-A		not specified	Uncertain significance (May 03, 2023)
10-103455621-G-T		not specified	Uncertain significance (Jan 17, 2024)
10-103455665-G-A		not specified	Uncertain significance (Mar 04, 2024)
10-103455686-C-T		not specified	Uncertain significance (Aug 01, 2022)
10-103455702-C-T		not specified	Uncertain significance (May 03, 2023)
10-103458238-C-G		not specified	Uncertain significance (Aug 12, 2021)
10-103458267-G-A		not specified	Uncertain significance (Feb 06, 2024)
10-103458277-C-T		not specified	Uncertain significance (Sep 01, 2021)
10-103458291-C-T			Likely pathogenic (Sep 27, 2016)
10-103458295-C-T			Benign (Mar 02, 2018)
10-103458336-C-G		not specified	Uncertain significance (May 04, 2022)
10-103458349-C-T		not specified	Uncertain significance (Jan 23, 2024)
10-103458399-G-A		not specified	Uncertain significance (Sep 13, 2023)
10-103458423-G-A		not specified	Uncertain significance (Jan 24, 2024)
10-103458433-C-T		not specified	Uncertain significance (Oct 20, 2021)

GnomAD

Source: gnomAD

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: dbNSFP

• 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