CALHM5

calcium homeostasis modulator family member 5, the group of Calcium homeostasis modulators

Basic information

Region (hg38): 6:116511638-116524788

Previous symbols: [ "C6orf188", "FAM26E" ]

Links

ENSG00000178033 ∙ NCBI:254228 ∙ ∙ HGNC:21568 ∙ Uniprot:Q8N5C1 ∙ 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 CALHM5 gene.

• Inborn genetic diseases (3 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CALHM5 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			2	1		3
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	2	1	0

Variants in CALHM5

This is a list of pathogenic ClinVar variants found in the CALHM5 region.

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

Position	Type	Phenotype	Significance	ClinVar
6-116511877-G-C		not specified	Uncertain significance (Jul 30, 2023)
6-116511884-T-C		not specified	Uncertain significance (Jan 02, 2024)
6-116511890-T-C		not specified	Likely benign (Feb 10, 2023)
6-116511966-A-T		not specified	Uncertain significance (Dec 14, 2023)
6-116512006-A-G		not specified	Uncertain significance (Sep 01, 2021)
6-116512039-C-G		not specified	Uncertain significance (Mar 11, 2022)
6-116512083-G-A		not specified	Uncertain significance (Jul 06, 2021)
6-116512169-G-A		not specified	Uncertain significance (Apr 15, 2022)
6-116512208-T-C		not specified	Uncertain significance (Jan 23, 2024)
6-116512226-C-T		not specified	Uncertain significance (Jul 21, 2021)
6-116515616-T-C		not specified	Uncertain significance (Apr 06, 2022)
6-116515628-C-T		not specified	Uncertain significance (Aug 12, 2021)
6-116515631-C-G		not specified	Uncertain significance (Dec 21, 2022)
6-116515663-C-T		not specified	Uncertain significance (Oct 05, 2021)
6-116515703-G-C		not specified	Uncertain significance (Jul 08, 2022)
6-116515832-C-T		not specified	Uncertain significance (Sep 06, 2022)
6-116515919-A-G		not specified	Uncertain significance (Jan 23, 2023)
6-116515925-T-C		not specified	Uncertain significance (Jan 03, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CALHM5	protein_coding	protein_coding	ENST00000368599	2	13147

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00102	0.833	125703	0	32	125735	0.000127

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.00518	164	164	1.00	0.00000824	2034
Missense in Polyphen		48	52.654	0.91162		669
Synonymous	-1.16	80	67.8	1.18	0.00000379	607
Loss of Function	1.19	6	10.1	0.595	5.12e-7	119

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000391	0.000391
Ashkenazi Jewish	0.00	0.00
East Asian	0.000109	0.000109
Finnish	0.00	0.00
European (Non-Finnish)	0.000141	0.000141
Middle Eastern	0.000109	0.000109
South Asian	0.000131	0.000131
Other	0.000164	0.000163

dbNSFP

Source: dbNSFP

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

Intolerance Scores

• rvis_EVS: 0.33
• rvis_percentile_EVS: 73.41

Haploinsufficiency Scores

• pHI: 0.564
• hipred: N
• hipred_score: 0.350
• ghis: 0.557

Essentials

• essential_gene_gene_trap: N

Mouse Genome Informatics

• Gene name: Calhm5

Gene ontology

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