CALHM2

calcium homeostasis modulator family member 2, the group of Calcium homeostasis modulators

Basic information

Region (hg38): 10:103446785-103452402

Previous symbols: [ "FAM26B" ]

Links

ENSG00000138172 ∙ NCBI:51063 ∙ OMIM:612235 ∙ HGNC:23493 ∙ Uniprot:Q9HA72 ∙ 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 CALHM2 gene.

• Inborn genetic diseases (19 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CALHM2 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			19			19
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	19	0	0

Variants in CALHM2

This is a list of pathogenic ClinVar variants found in the CALHM2 region.

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

Position	Type	Phenotype	Significance	ClinVar
10-103447178-C-G		not specified	Uncertain significance (Dec 16, 2023)
10-103447184-C-T		not specified	Uncertain significance (Sep 27, 2021)
10-103447274-C-T		not specified	Uncertain significance (Jun 16, 2023)
10-103447313-C-T		not specified	Uncertain significance (Jul 31, 2023)
10-103447397-C-T		not specified	Uncertain significance (Aug 10, 2021)
10-103447414-A-T		not specified	Uncertain significance (Dec 26, 2023)
10-103447426-C-G		not specified	Uncertain significance (Nov 14, 2023)
10-103447466-A-G		not specified	Uncertain significance (Jun 03, 2022)
10-103447481-G-A		not specified	Uncertain significance (Nov 27, 2023)
10-103447511-G-A		not specified	Uncertain significance (Nov 18, 2022)
10-103447531-A-G		not specified	Uncertain significance (Dec 17, 2021)
10-103449409-C-T		not specified	Uncertain significance (Oct 05, 2022)
10-103449410-G-A		not specified	Uncertain significance (Feb 27, 2023)
10-103449450-C-G		not specified	Uncertain significance (Nov 13, 2023)
10-103449498-G-C		not specified	Uncertain significance (Apr 04, 2023)
10-103449529-G-A		not specified	Uncertain significance (Sep 15, 2022)
10-103449536-C-T		not specified	Uncertain significance (Jan 19, 2024)
10-103449560-A-G		not specified	Uncertain significance (Feb 17, 2022)
10-103449591-C-A		not specified	Uncertain significance (Feb 22, 2023)
10-103449613-G-A		not specified	Uncertain significance (Aug 12, 2021)
10-103449616-C-T		not specified	Uncertain significance (Oct 29, 2021)
10-103449617-G-A		not specified	Uncertain significance (May 18, 2023)
10-103449689-C-G		not specified	Uncertain significance (Dec 14, 2023)
10-103449766-G-A		not specified	Uncertain significance (Sep 13, 2023)
10-103449773-C-T		not specified	Uncertain significance (Feb 17, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CALHM2	protein_coding	protein_coding	ENST00000260743	2	6118

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00000831	0.323	122725	38	2984	125747	0.0121

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.108	213	209	1.02	0.0000149	2085
Missense in Polyphen		74	76.822	0.96327		767
Synonymous	-0.409	100	94.9	1.05	0.00000692	703
Loss of Function	0.179	8	8.56	0.934	3.70e-7	101

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00931	0.00931
Ashkenazi Jewish	0.0156	0.0157
East Asian	0.000326	0.000326
Finnish	0.0352	0.0353
European (Non-Finnish)	0.0153	0.0152
Middle Eastern	0.000326	0.000326
South Asian	0.000817	0.000817
Other	0.0143	0.0143

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Pore-forming subunit of a voltage-gated ion channel. {ECO:0000250|UniProtKB:Q8IU99}.

Recessive Scores

• pRec: 0.111

Intolerance Scores

• loftool: 0.722
• rvis_EVS: 0.06
• rvis_percentile_EVS: 58.74

Haploinsufficiency Scores

• pHI: 0.145
• hipred: N
• hipred_score: 0.350
• ghis: 0.511

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.390

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Calhm2

Gene ontology

• Biological process: ion transport
• Cellular component: integral component of plasma membrane