CALHM6

calcium homeostasis modulator family member 6, the group of Calcium homeostasis modulators

Basic information

Region (hg38): 6:116461370-116463771

Previous symbols: [ "C6orf187", "FAM26F" ]

Links

ENSG00000188820 ∙ NCBI:441168 ∙ OMIM:617305 ∙ HGNC:33391 ∙ Uniprot:Q5R3K3 ∙ 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 CALHM6 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CALHM6 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				1		1
missense			29			29
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	29	1	0

Variants in CALHM6

This is a list of pathogenic ClinVar variants found in the CALHM6 region.

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

Position	Type	Phenotype	Significance	ClinVar
6-116461933-G-A		not specified	Uncertain significance (Nov 24, 2024)
6-116462036-C-A		not specified	Uncertain significance (Nov 22, 2024)
6-116462044-T-C		not specified	Uncertain significance (Jul 02, 2024)
6-116462075-T-C		not specified	Uncertain significance (Sep 13, 2023)
6-116462083-G-A		not specified	Uncertain significance (Apr 17, 2024)
6-116462113-G-T		not specified	Uncertain significance (Jun 29, 2023)
6-116462119-T-C		not specified	Uncertain significance (Jun 03, 2022)
6-116462126-T-G		not specified	Uncertain significance (Dec 20, 2023)
6-116462132-A-G		not specified	Uncertain significance (Dec 18, 2023)
6-116462146-C-G		not specified	Uncertain significance (Nov 08, 2024)
6-116462165-C-T		not specified	Uncertain significance (Oct 29, 2024)
6-116462196-C-G		not specified	Uncertain significance (Aug 14, 2024)
6-116462259-C-T			Likely benign (Nov 01, 2022)
6-116462261-T-C		not specified	Uncertain significance (Jul 25, 2023)
6-116462266-T-C		not specified	Uncertain significance (May 09, 2024)
6-116462358-C-A		not specified	Uncertain significance (May 31, 2023)
6-116462359-C-A		not specified	Uncertain significance (Jul 14, 2021)
6-116462362-A-C		not specified	Uncertain significance (Oct 29, 2024)
6-116462386-G-C		not specified	Uncertain significance (Sep 29, 2022)
6-116462390-C-G		not specified	Uncertain significance (Jan 08, 2024)
6-116462390-C-T		not specified	Uncertain significance (Dec 20, 2021)
6-116462393-G-A		not specified	Uncertain significance (Mar 21, 2023)
6-116463317-T-C		not specified	Uncertain significance (Mar 24, 2023)
6-116463407-A-G		not specified	Uncertain significance (Nov 14, 2024)
6-116463426-T-G		not specified	Uncertain significance (Jan 09, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CALHM6	protein_coding	protein_coding	ENST00000368605	2	2402

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00946	0.609	118177	0	1	118178	0.00000423

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.192	128	134	0.953	0.00000633	1970
Missense in Polyphen		34	45.675	0.74439		701
Synonymous	0.742	54	61.4	0.880	0.00000308	653
Loss of Function	0.312	3	3.64	0.824	1.57e-7	50

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.00000913	0.00000913
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

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

Haploinsufficiency Scores

• pHI: 0.0578
• hipred: N
• hipred_score: 0.123

Essentials

• essential_gene_gene_trap: N

Mouse Genome Informatics

• Gene name: Calhm6

Gene ontology

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