FAT3

Chr 11

FAT atypical cadherin 3

Also known as: CDHF15, CDHR10, hFat3

NCBI Gene: 120114 ENSG00000165323 UniProt: Q8TDW7

Predicted to enable calcium ion binding activity. Predicted to be involved in cell-cell adhesion mediated by cadherin. Predicted to act upstream of or within several processes, including negative regulation of dendrite development; neuron migration; and retina layer formation. Predicted to be located in dendrite and membrane. Predicted to be active in adherens junction and plasma membrane. [provided by Alliance of Genome Resources, Jun 2026]

Research

ResearchGenerating clinical summary…

Clinical highlights

Interpreting a novel variant

This gene is strongly intolerant of loss-of-function variation in the population, so LoF variants warrant close attention. No curated mechanism annotation is available — see the mechanism card for the computational prediction and its caveats.Based on population constraint only.

Active trials

Pubs (1 yr)

—

P/LP submissions

—

P/LP missense

0.25

LOEUF· LoF intol.

LOF

Mechanism· predicted

Some data sources returned errors (1)

omim: Error: OMIM fetch failed: 429

Population Genetics & Constraint

gnomAD v4 — loss-of-function & missense intolerance

gnomAD

LoF intolerant — likely haploinsufficient

LoF Constraint?

0.25LOEUF

pLI 1.000

Z-score 8.93

OE 0.18 (0.13–0.25)

Highly constrained

Highly LoF-intolerant (top ~10% of genes)

Missense Constraint?

1.26Z-score

OE missense 0.93 (0.90–0.96)

2345 obs / 2523.1 exp

Tolerant

Mild missense constraint

Observed / Expected Ratios?

LoF OE?0.18 (0.13–0.25)

0≤0.351.4

Missense OE?0.93 (0.90–0.96)

0≤0.61.4

Synonymous OE?1.05

0≤1.21.6

LoF obs/exp: 25 / 138.3Missense obs/exp: 2345 / 2523.1Syn Z: -1.29

Background carrier burden — how many people carry a rare variant somewhere in FAT3?

gnomAD v4 · ~731k individuals · PASS only

Rare means allele frequency under

Rare missense

1 in 11

5,821 rare PASS variants

Rare truncating (LoF)

1 in 1,000

269 rare PASS variants

Rare synonymous (reference)

1 in 15

2,473 rare PASS variants

Truncating variants are far rarer here than missense — that gap, in human units, is what constraint means for FAT3. A background rate for each class, not the frequency of any particular variant; thin-coverage exons undercount.

By genetic ancestry · 9 gnomAD groups · rare = under 0.1% in that group

Group	People	Missense	Truncating
European (non-Finnish)	~556k	1 in 14	1 in 1,000
South Asian	~43k	1 in 11	1 in 360
Remaining (unassigned)	~30k	1 in 11	1 in 390
European (Finnish)	~27k	1 in 43	1 in 1,500
Admixed American	~22k	1 in 10	1 in 1,500
African / African American	~21k	1 in 11	1 in 890
East Asian	~20k	1 in 14	1 in 1,100
Ashkenazi Jewish	~13k	1 in 46	1 in 750
Middle Eastern	~2,884	1 in 13	none seen

Each group is summed over the variants that are rare in that group. Grey ≈ figures rest on fewer than five expected carriers — too few to distinguish groups. Differences mostly reflect how many people were sampled and how much variation each ancestry carries, not disease risk.

Exome coverage (gnomAD): 25 of 27 coding exons well covered in gnomAD exomes; exons 26, 27 poorly covered. Genomes: all 27.? see exons ↓