FAAP20

Chr 1

FA core complex associated protein 20

Also known as: C1orf86, FP7162

NCBI Gene: 199990 ENSG00000162585 UniProt: Q6NZ36 OMIM: 615183

The protein is a component of the Fanconi anemia complex that recognizes ubiquitin modifications at DNA interstrand cross-links and recruits other repair factors to promote DNA repair and translesion synthesis. Mutations cause Fanconi anemia, a disorder characterized by bone marrow failure, developmental abnormalities, and cancer predisposition with autosomal recessive inheritance. The gene shows moderate constraint against loss-of-function variants (LOEUF 0.751), reflecting its essential role in DNA repair.

OMIM ResearchSummary from RefSeq, UniProt

Enables K63-linked polyubiquitin modification-dependent protein binding activity and ubiquitin-modified protein reader activity. Involved in interstrand cross-link repair and translesion synthesis. Located in chromatin and nuclear body. Part of Fanconi anaemia nuclear complex. [provided by Alliance of Genome Resources, Jun 2026]

OMIM 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

0.75

LOEUF

—

Mechanism

Population Genetics & Constraint

gnomAD v4 — loss-of-function & missense intolerance

gnomAD

Moderate LoF intolerance

LoF Constraint?

0.75LOEUF

pLI 0.526

Z-score 1.96

OE 0.16 (0.06–0.75)

Moderately constrained

Typical tolerance to LoF variation

Missense Constraint?

0.20Z-score

OE missense 0.95 (0.81–1.12)

102 obs / 107.8 exp

Tolerant

Mild missense constraint

Observed / Expected Ratios?

LoF OE?0.16 (0.06–0.75)

0≤0.351.4

Missense OE?0.95 (0.81–1.12)

0≤0.61.4

Synonymous OE?1.14

0≤1.21.6

LoF obs/exp: 1 / 6.3Missense obs/exp: 102 / 107.8Syn Z: -0.77

Background carrier burden — how many people carry a rare variant somewhere in FAAP20?

gnomAD v4 · ~730k individuals · PASS only

Rare means allele frequency under

Rare missense

1 in 73

507 rare PASS variants

Rare truncating (LoF)

1 in 1,000

106 rare PASS variants

Rare synonymous (reference)

1 in 370

110 rare PASS variants

Truncating variants are far rarer here than missense — that gap, in human units, is what constraint means for FAAP20. 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 99	1 in 1,200
South Asian	~43k	1 in 87	1 in 530
Remaining (unassigned)	~30k	1 in 51	1 in 1,700
European (Finnish)	~26k	1 in 430	≈ 1 in 6,200
Admixed American	~22k	1 in 61	1 in 1,900
African / African American	~21k	1 in 63	1 in 700
East Asian	~20k	1 in 140	1 in 710
Ashkenazi Jewish	~13k	1 in 220	≈ 1 in 13,000
Middle Eastern	~2,884	1 in 110	≈ 1 in 1,400

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): 3 of 4 coding exons well covered in gnomAD exomes; exon 1 marginal. Genomes: 3 of 4 (exon 1 below).? see exons ↓