CACHD1

protein-coding

cache domain containing 1, the group of MicroRNA protein coding host genes

Gene summary

Predicted to enable voltage-gated calcium channel activity. Predicted to be involved in calcium ion transmembrane transport. Predicted to be located in membrane. Predicted to be part of voltage-gated calcium channel complex. [provided by Alliance of Genome Resources, Jul 2025]

Previous symbols:

VWCD1

MANE transcript

NM_020925.4

Inheritance

—

ClinVar variants

P:9U:169B:4

Top phenotype

Inborn genetic diseases

gnomAD constraint

pLI —, LoF o/e 0.41

Max pathogenic AF

—

Genomic locus

chr1:64,470,129-64,693,058

External References & Databases

Ensembl (ENSG00000158966)

Transcript & Mutation Effects

hg38 • Region Span ~222.9 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to CACHD1 variants in ClinVar

3 Conditions Cataloged

Inborn genetic diseasesTotal: 158

DAVIS-WELLS SYNDROMETotal: 9

not providedTotal: 6

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_020925.4. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous			2 clinvar	3 clinvar		5
missense			162 clinvar	1 clinvar		163
nonsense	2 clinvar	2 clinvar				4
start loss						0
frameshift	2 clinvar					2
splice donor/acceptor (+/-2bp)	3 clinvar		5 clinvar			8
Total	7	2	169	4	0	182

Highest pathogenic variant AF is 0.00002880657

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 30 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_020925.4	RefSeq	NP_065976.3	27	MANE Select
ENST00000651257.2	Ensembl	ENSP00000498498.1	27	MANE Select
NM_001293274.2	RefSeq	NP_001280203.1	21	Standard
ENST00000290039.6	Ensembl	ENSP00000290039.5	27	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

calcium ion transmembrane transport

Molecular Function

voltage-gated calcium channel activity

Cellular Component

voltage-gated calcium channel complex

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000290039
Coding exons: 27
Length: 222314
Individuals with no LoFs: 125694
Homozygous LoFs: 0
Heterozygous LoFs: 54
Defined: 125748
p: 0.000215

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	1.71	579	707	0.819	0.0000394	8097
Missense (PolyPhen)		107	175.57	0.60944		2018
Synonymous	0.718	250	265	0.944	0.0000157	2329
Loss of Function	4.28	25	61.1	0.409	0.00000328	705

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00018	0.00018	rare
Latino/Admixed American	0.00023	0.00023	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0.00028	0.00027	rare
Finnish	0.00014	0.00014	rare
European (Non-Finnish)	0.00019	0.00018	rare
South Asian	0.00043	0.00042	rare
Other	0.00017	0.00016	rare

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: May regulate voltage-dependent calcium channels. {ECO:0000250}.;

Recessive Scores

pRec: 0.109

Intolerance Scores

LoFtool: 0.614
RVIS EVS: -1.74
RVIS percentile EVS: 2.42

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.348

Gene Damage Prediction

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