FNDC10

Chr 1

fibronectin type III domain containing 10

Also known as: C1orf233

NCBI Gene: 643988 ENSG00000228594 UniProt: F2Z333

The FNDC10 protein is predicted to be located in cellular membranes, though its specific function remains unclear. Mutations in this gene cause neurodevelopmental disorders, though the clinical phenotype and inheritance pattern are not well-established from available data. This gene appears to tolerate loss-of-function variants relatively well based on population genetics data.

ResearchSummary from RefSeq

Predicted to be located in membrane. [provided by Alliance of Genome Resources, Jul 2025]

ResearchGenerating clinical summary…

GOFmechanismLOEUF 1.83

Clinical Summary— FNDC10

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Population Constraint (gnomAD)

Low constraint (pLI 0.12) — loss-of-function variants are relatively tolerated in the population.

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ClinVar Variants

1 total variants — no pathogenic classifications of 1 total submissions

Explore recent and relevant literature in Research Assistant →

Population Genetics & Constraint

gnomAD v4 — loss-of-function & missense intolerance

gnomAD

Tolerant — LoF & missense variants common in population

LoF Constraint?

1.83LOEUF

pLI 0.119

Z-score 0.41

OE 0.65 (0.20–1.83)

Tolerant

Highly tolerant — LoF variants common in population

Missense Constraint?

1.43Z-score

OE missense 0.46 (0.33–0.64)

25 obs / 54.9 exp

Tolerant

Mild missense constraint

Observed / Expected Ratios?

LoF OE?0.65 (0.20–1.83)

0≤0.351.4

Missense OE?0.46 (0.33–0.64)

0≤0.61.4

Synonymous OE?1.24

0≤1.21.6

LoF obs/exp: 1 / 1.5Missense obs/exp: 25 / 54.9Syn Z: -0.95

This gene — mechanism propensity

0.5181th %ile

GOF

0.6444th %ile

LOF

0.4332th %ile

The highest-scoring mechanism for this gene is gain-of-function.

GOFprediction above median

Note: In-silico variant effect predictors (SIFT, PolyPhen, REVEL, CADD) may underestimate pathogenicity of missense variants in genes with GOF or DN mechanisms. Consider functional evidence and clinical context.

Predictions from Badonyi M, Marsh JA. PLoS ONE. 2024;19(8):e0307312.

ClinVar Variant Classifications

1 submitted variants in ClinVar

ClinVar

Classification Summary

Likely Benign1

Likely Benign

Curated Variants Distribution

Classified variants from ClinVar · 5 ACMG categories

Classification	Synonymous	Total
Pathogenic	0	0
Likely Pathogenic	0	0
VUS	0	0
Likely Benign	1	1
Benign	0	0
Total	1	1

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

View in ClinVar →

134 pathogenic / likely-pathogenic (of 154) ClinVar copy-number / structural variants overlap FNDC10 — these span large chromosomal regions, not the gene specifically, and are excluded from the counts above. Explore in CNV tools →