Heavy data lifting in progress

Harmonizing cross-database IDs...

CACFD1

Chr 9

calcium channel flower domain containing 1

Also known as: C9orf7, D9S2135, FLOWER

NCBI Gene: 11094 ENSG00000160325 UniProt: Q9UGQ2

Predicted to be involved in vesicle-mediated transport. Predicted to be located in several cellular components, including Golgi apparatus; cytoplasmic vesicle; and endoplasmic reticulum membrane. [provided by Alliance of Genome Resources, Jul 2025]

105

ClinVar variants

36

Pathogenic / LP

0.00

pLI score

0

Active trials

Clinical Summary— CACFD1

⚡

Population Constraint (gnomAD)

Low constraint (pLI 0.00) — loss-of-function variants are relatively tolerated in the population.

📋

ClinVar Variants

36 Pathogenic / Likely Pathogenic· 55 VUS of 105 total submissions

Population Genetics & Constraint

gnomAD v4 — loss-of-function & missense intolerance

Tolerant — LoF & missense variants common in population

LoF Constraint?LOEUF (Loss-of-function Observed/Expected Upper bound Fraction) is the upper bound of the 90% CI for LoF OE — the preferred gnomAD v4 metric. Lower = more intolerant to LoF. LOEUF < 0.35 = highly constrained.

1.24LOEUF

pLI 0.001

Z-score 1.07

OE 0.63 (0.34–1.24)

Tolerant

Highly tolerant — LoF variants common in population

Missense Constraint?Missense Z-score: standard deviations fewer missense variants observed vs. expected. Z > 3.09 (p < 0.001) = gene does not tolerate missense variation. OE missense < 0.6 is also considered constrained.

0.15Z-score

OE missense 0.96 (0.84–1.11)

134 obs / 138.9 exp

Tolerant

Mild missense constraint

Observed / Expected Ratios?Shaded band = 90% confidence interval. Vertical tick = point estimate. Grey threshold line = gnomAD constraint cutoff for that variant class.

LoF OE?Ratio of observed to expected LoF variants. Upper CI bound (LOEUF) ≤ 0.35 = strong LoF constraint signal.0.63 (0.34–1.24)

0≤0.351.4

Missense OE?Ratio of observed to expected missense variants. OE ≤ 0.6 = fewer missense variants than expected by chance.0.96 (0.84–1.11)

0≤0.61.4

Synonymous OE?Control metric — synonymous variants are largely neutral and expected near OE = 1.0. Significant deviation may indicate annotation issues.1.06

0≤1.21.6

LoF obs/exp: 6 / 9.6Missense obs/exp: 134 / 138.9Syn Z: -0.39

ClinVar Variant Classifications

105 submitted variants in ClinVar

Classification Summary

Pathogenic35

Likely Pathogenic1

VUS55

Likely Benign3

35

Pathogenic

1

Likely Pathogenic

55

VUS

3

Likely Benign

Curated Variants Distribution

Classified variants from ClinVar · 5 ACMG categories

Classification	LoF	Missense + Inframe	Non-coding	Synonymous	Total
Pathogenic	0	0	35	0	35
Likely Pathogenic	0	0	1	0	1
VUS	0	47	8	0	55
Likely Benign	0	3	0	0	3
Benign	0	0	0	0	0
Total	0	50	44	0	94

LoF = frameshift, stop gained/lost, canonical splice · Counts from ClinVar esearch · Updated hourly

View in ClinVar →

Protein Context — Lollipop Plot

CACFD1 · protein map & ClinVar variants

Showing all ClinVar variants across the protein. Search a specific variant to highlight its position.

OMIM — Genotype-Phenotype Relationships

1 OMIM entry

CALCIUM CHANNEL FLOWER-DOMAIN CONTAINING PROTEIN 1; CACFD1

MIM #613104 · *

External Resources

Links to major genomics databases and tools

Variant Interpretation

Variant interpretation & classification platform

Franklin by Genoox

AI-powered variant curation and clinical analysis

Genomic literature search for variants and genes

ACMG/AMP variant classification tool

Population Databases

Population allele frequencies & constraint metrics

Genomic variants and phenotypes in rare disease patients

Clinical variant interpretations from submitters worldwide

Short genetic variation database

Gene Resources

Gene annotation, transcripts & comparative genomics

Comprehensive gene information and references

Protein sequence, structure and function

Online Mendelian Inheritance in Man

Human gene compendium

Gene expression across human tissues

Expert Curation

Expert-curated gene-disease validity

Gene Curation Coalition — multi-curator classifications

Rare disease encyclopedia and gene-disease associations

Autism-gene association scoring (SFARI)

Gene panels for rare disease diagnostics (Genomics England)

Leiden Open Variation Database — variant listings

Expert-authored summaries of heritable conditions (NCBI)

Clinical Literature

Landmark / reviewRecent case evidence

Key Publications

Landmark & review papers · by relevance

PubMed

Identification of genetic loci jointly influencing COVID-19 and coronary heart diseases.

Wang S et al.·Hum Genomics

2023

Genome-wide meta-analysis associates GPSM1 with type 2 diabetes, a plausible gene involved in skeletal muscle function.

Ding Q et al.·J Hum Genet

2020Meta-analysis

Top 10 resultsSearch PubMed ↗

Recent Gene-Specific Literature

Gene in title · MEDLINE · newest first

Europe PMC

No open access results found

Top 5 resultsSearch Europe PMC ↗

Clinical Trials

Active and recruiting trials from ClinicalTrials.gov

ClinicalTrials.gov

No active trials found for this gene.

Search ClinicalTrials.gov →

External Resources

Links to major genomics databases and tools

Variant Interpretation

Variant interpretation & classification platform

Franklin by Genoox

AI-powered variant curation and clinical analysis

Genomic literature search for variants and genes

ACMG/AMP variant classification tool

Population Databases

Population allele frequencies & constraint metrics

Genomic variants and phenotypes in rare disease patients

Clinical variant interpretations from submitters worldwide

Short genetic variation database

Gene Resources

Gene annotation, transcripts & comparative genomics

Comprehensive gene information and references

Protein sequence, structure and function

Online Mendelian Inheritance in Man

Human gene compendium

Gene expression across human tissues

Expert Curation

Expert-curated gene-disease validity

Gene Curation Coalition — multi-curator classifications

Rare disease encyclopedia and gene-disease associations

Autism-gene association scoring (SFARI)

Gene panels for rare disease diagnostics (Genomics England)

Leiden Open Variation Database — variant listings

Expert-authored summaries of heritable conditions (NCBI)