CACHD1

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

Basic information

Region (hg38): 1:64470129-64693058

Previous symbols: [ "VWCD1" ]

Links

ENSG00000158966 ∙ NCBI:57685 ∙ OMIM:620144 ∙ HGNC:29314 ∙ Uniprot:Q5VU97 ∙ 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 CACHD1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CACHD1 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				2		2
missense			86	1		87
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region				1		1
non coding						0
Total	0	0	86	3	0

Variants in CACHD1

This is a list of pathogenic ClinVar variants found in the CACHD1 region.

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

Position	Type	Phenotype	Significance	ClinVar
1-64470928-G-T		Inborn genetic diseases	Uncertain significance (Aug 10, 2021)
1-64470938-T-C		Inborn genetic diseases	Uncertain significance (Oct 09, 2024)
1-64550612-G-A		Inborn genetic diseases	Uncertain significance (Jan 10, 2025)
1-64550627-A-G		Inborn genetic diseases	Uncertain significance (Dec 08, 2023)
1-64582172-G-T		Inborn genetic diseases	Uncertain significance (Dec 20, 2024)
1-64582184-A-G		Inborn genetic diseases	Uncertain significance (Jan 04, 2024)
1-64582187-G-A		Inborn genetic diseases	Uncertain significance (Dec 28, 2022)
1-64582190-A-T		Inborn genetic diseases	Uncertain significance (Apr 26, 2024)
1-64582237-A-G		Inborn genetic diseases	Uncertain significance (Mar 20, 2024)
1-64582238-C-T		Inborn genetic diseases	Uncertain significance (May 23, 2023)
1-64582268-T-C		Inborn genetic diseases	Uncertain significance (Aug 30, 2021)
1-64582282-A-G		Inborn genetic diseases	Uncertain significance (May 23, 2023)
1-64582291-C-T		Inborn genetic diseases	Uncertain significance (Jan 03, 2025)
1-64602856-G-A		Inborn genetic diseases	Uncertain significance (Jun 12, 2023)
1-64602864-A-G		Inborn genetic diseases	Uncertain significance (Jun 24, 2022)
1-64602879-C-T		Inborn genetic diseases	Uncertain significance (Feb 18, 2025)
1-64629451-G-A		Inborn genetic diseases	Uncertain significance (Sep 22, 2023)
1-64632622-G-A		Inborn genetic diseases	Uncertain significance (Dec 12, 2024)
1-64632660-G-A		Inborn genetic diseases	Uncertain significance (May 10, 2024)
1-64632666-T-G		Inborn genetic diseases	Uncertain significance (Aug 08, 2023)
1-64632679-C-T		Inborn genetic diseases	Uncertain significance (Dec 27, 2023)
1-64632723-G-A		Inborn genetic diseases	Uncertain significance (Jan 20, 2025)
1-64632736-A-G		Inborn genetic diseases	Uncertain significance (Jan 18, 2025)
1-64634071-G-A		Inborn genetic diseases	Uncertain significance (Feb 28, 2024)
1-64634074-C-T		Inborn genetic diseases	Uncertain significance (Jan 29, 2025)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CACHD1	protein_coding	protein_coding	ENST00000290039	27	222314

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
5.83e-9	1.00	125694	0	54	125748	0.000215

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.71	579	707	0.819	0.0000394	8097
Missense in 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

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000416	0.000416
Ashkenazi Jewish	0.00	0.00
East Asian	0.000281	0.000272
Finnish	0.000139	0.000139
European (Non-Finnish)	0.000186	0.000185
Middle Eastern	0.000281	0.000272
South Asian	0.000428	0.000425
Other	0.000165	0.000163

dbNSFP

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

Haploinsufficiency Scores

• pHI: 0.662
• hipred: Y
• hipred_score: 0.540
• ghis: 0.590

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.348

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Cachd1

Gene ontology

• Biological process: calcium ion transmembrane transport
• Cellular component: voltage-gated calcium channel complex
• Molecular function: voltage-gated calcium channel activity