CACFD1

calcium channel flower domain containing 1

Basic information

Region (hg38): 9:133459964-133470848

Previous symbols: [ "C9orf7" ]

Links

ENSG00000160325 ∙ NCBI:11094 ∙ OMIM:613104 ∙ HGNC:1365 ∙ Uniprot:Q9UGQ2 ∙ 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 CACFD1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CACFD1 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			12			12
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding			2			2
Total	0	0	16	0	0

Variants in CACFD1

This is a list of pathogenic ClinVar variants found in the CACFD1 region.

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

Position	Type	Phenotype	Significance	ClinVar
9-133460091-G-A		not specified	Uncertain significance (Feb 17, 2022)
9-133460153-G-T		not specified	Uncertain significance (Feb 22, 2023)
9-133460167-C-G		not specified	Uncertain significance (May 24, 2023)
9-133463488-G-A		not specified	Uncertain significance (May 15, 2024)
9-133463545-G-A		not specified	Uncertain significance (Jun 04, 2024)
9-133465354-C-T		not specified	Uncertain significance (Feb 27, 2023)
9-133465377-G-A		not specified	Uncertain significance (Jan 08, 2024)
9-133465392-G-A		not specified	Uncertain significance (Oct 06, 2021)
9-133465407-G-A		not specified	Uncertain significance (Nov 10, 2021)
9-133465417-G-A		not specified	Uncertain significance (Mar 19, 2024)
9-133467937-A-G		not specified	Uncertain significance (Feb 27, 2024)
9-133467962-C-T		not specified	Uncertain significance (May 11, 2022)
9-133468368-G-A		not specified	Uncertain significance (May 14, 2024)
9-133468566-C-G		not specified	Uncertain significance (Feb 28, 2023)
9-133468580-A-T		not specified	Uncertain significance (Jan 19, 2024)
9-133468626-C-T		not specified	Uncertain significance (Dec 14, 2021)
9-133468628-C-T		not specified	Uncertain significance (Jun 17, 2024)
9-133468641-G-C		not specified	Uncertain significance (Jun 18, 2021)
9-133468642-G-C		not specified	Uncertain significance (Feb 05, 2024)
9-133468665-C-T		not specified	Uncertain significance (Aug 14, 2023)
9-133468698-G-A		not specified	Uncertain significance (Jan 07, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CACFD1	protein_coding	protein_coding	ENST00000540581	6	10882

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.000806	0.793	125724	0	19	125743	0.0000756

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.148	134	139	0.965	0.00000826	1457
Missense in Polyphen		34	36.513	0.93117		353
Synonymous	-0.389	65	61.1	1.06	0.00000410	490
Loss of Function	1.07	6	9.58	0.626	4.09e-7	107

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000206	0.000206
Ashkenazi Jewish	0.000100	0.0000992
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000881	0.0000879
Middle Eastern	0.00	0.00
South Asian	0.0000653	0.0000653
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Pathway: Neuronal System;Presynaptic depolarization and calcium channel opening;Transmission across Chemical Synapses (Consensus)

Intolerance Scores

• rvis_EVS: -0.27
• rvis_percentile_EVS: 34.32

Haploinsufficiency Scores

• pHI: 0.187
• hipred: N
• hipred_score: 0.123
• ghis: 0.591

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.114

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Cacfd1
• Phenotype: homeostasis/metabolism phenotype; cellular phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); neoplasm

Gene ontology

• Biological process: biological_process;vesicle-mediated transport
• Cellular component: cellular_component;integral component of membrane
• Molecular function: molecular_function;protein binding