CALHM3

calcium homeostasis modulator 3, the group of Calcium homeostasis modulators

Basic information

Region (hg38): 10:103472804-103479240

Previous symbols: [ "FAM26A" ]

Links

ENSG00000183128 ∙ NCBI:119395 ∙ OMIM:618263 ∙ HGNC:23458 ∙ Uniprot:Q86XJ0 ∙ 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 CALHM3 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CALHM3 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			28			28
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	28	0	0

Variants in CALHM3

This is a list of pathogenic ClinVar variants found in the CALHM3 region.

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

Position	Type	Phenotype	Significance	ClinVar
10-103473220-T-G		not specified	Uncertain significance (May 05, 2023)
10-103473235-A-C		not specified	Uncertain significance (Feb 06, 2023)
10-103473280-C-A		not specified	Uncertain significance (Mar 06, 2023)
10-103473343-A-T		not specified	Uncertain significance (Jan 18, 2022)
10-103473346-A-G		not specified	Uncertain significance (Feb 05, 2024)
10-103473347-G-A		not specified	Uncertain significance (Apr 22, 2024)
10-103473443-C-G		not specified	Uncertain significance (Apr 25, 2023)
10-103473464-C-T		not specified	Uncertain significance (Jan 04, 2024)
10-103473479-G-C		not specified	Uncertain significance (May 06, 2024)
10-103473482-C-T		not specified	Uncertain significance (Apr 20, 2024)
10-103473505-G-A		not specified	Uncertain significance (Mar 29, 2022)
10-103473515-G-A		not specified	Uncertain significance (Aug 09, 2021)
10-103473544-G-A		not specified	Uncertain significance (Oct 05, 2022)
10-103473563-C-G		not specified	Uncertain significance (Sep 20, 2023)
10-103473583-A-G		not specified	Uncertain significance (Nov 20, 2023)
10-103473599-T-C		not specified	Uncertain significance (Jul 05, 2022)
10-103473628-T-C		not specified	Uncertain significance (Jan 03, 2022)
10-103473698-C-T		not specified	Uncertain significance (Jan 04, 2022)
10-103476316-C-T		not specified	Uncertain significance (May 26, 2024)
10-103476401-T-C		not specified	Uncertain significance (Aug 30, 2021)
10-103476512-C-T		not specified	Uncertain significance (Mar 02, 2023)
10-103476541-C-T		not specified	Uncertain significance (Sep 27, 2022)
10-103478770-C-T		not specified	Uncertain significance (Jun 01, 2023)
10-103478788-C-T		not specified	Uncertain significance (Oct 25, 2022)
10-103478798-C-T		not specified	Uncertain significance (Jun 06, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CALHM3	protein_coding	protein_coding	ENST00000369783	3	6437

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00331	0.842	0	0	0	0	0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.347	186	200	0.931	0.0000138	2182
Missense in Polyphen		75	69.377	1.081		760
Synonymous	0.983	83	95.2	0.872	0.00000652	753
Loss of Function	1.18	5	8.79	0.569	3.76e-7	101

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)	0.00	0.00
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}.

Recessive Scores

• pRec: 0.0963

Intolerance Scores

• rvis_EVS: -0.05
• rvis_percentile_EVS: 49.39

Haploinsufficiency Scores

• pHI: 0.161

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.355

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Calhm3

Gene ontology

• Biological process: ion transport
• Cellular component: integral component of plasma membrane
• Molecular function: protein binding