CACFD1

protein-coding

calcium channel flower domain containing 1

Gene summary

Predicted to be involved in vesicle-mediated transport. Predicted to act upstream of or within endocytosis. Predicted to be located in Golgi apparatus; cytoplasmic vesicle; and endoplasmic reticulum membrane. Predicted to be active in plasma membrane; synapse; and vesicle. [provided by Alliance of Genome Resources, Jun 2026]

Previous symbols:

C9orf7

MANE transcript

NM_017586.5

Inheritance

—

ClinVar variants

U:43B:3

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.63

Max pathogenic AF

—

Genomic locus

chr9:133,459,965-133,470,848

External References & Databases

Ensembl (ENSG00000160325)

Transcript & Mutation Effects

hg38 • Region Span ~10.9 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 CACFD1 variants in ClinVar

1 Conditions Cataloged

not specifiedTotal: 46

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_017586.5. 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			6 clinvar			6
missense			35 clinvar	3 clinvar		38
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			2 clinvar			2
Total	0	0	43	3	0	46

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 33 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_017586.5	RefSeq	NP_060056.1	5	MANE Select
ENST00000316948.9	Ensembl	ENSP00000317121.4	5	MANE Select
NM_001135775.4	RefSeq	NP_001129247.1	4	Standard
NM_001242369.2	RefSeq	NP_001229298.1	6	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

Neuronal System
Presynaptic depolarization and calcium channel opening
Transmission across Chemical Synapses

Biological Process

biological_process
vesicle-mediated transport

Molecular Function

molecular_function
protein binding

Cellular Component

cellular_component
integral component of membrane

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000540581
Coding exons: 6
Length: 10882
Individuals with no LoFs: 125724
Homozygous LoFs: 0
Heterozygous LoFs: 19
Defined: 125743
p: 0.0000756

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.148	134	139	0.965	0.00000826	1457
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0.000062	0.000062	rare
Latino/Admixed American	0.00014	0.00014	rare
Ashkenazi Jewish	0.00010	0.000099	rare
East Asian	0	0.0	absent
Finnish	0	0.0	absent
European (Non-Finnish)	0.000088	0.000088	rare
South Asian	0.000065	0.000065	rare
Other	0	0.0	absent

dbNSFP Gene Annotations

Source: dbNSFP

Intolerance Scores

RVIS EVS: -0.27
RVIS percentile EVS: 34.32

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.114

Gene Damage Prediction

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