CRABP2

Chr 1

cellular retinoic acid binding protein 2

Also known as: CRABP-II, RBP6

NCBI Gene: 1382 ENSG00000143320 UniProt: P29373 OMIM: 180231

This gene encodes a member of the retinoic acid (RA, a form of vitamin A) binding protein family and lipocalin/cytosolic fatty-acid binding protein family. The protein is a cytosol-to-nuclear shuttling protein, which facilitates RA binding to its cognate receptor complex and transfer to the nucleus. It is involved in the retinoid signaling pathway, and is associated with increased circulating low-density lipoprotein cholesterol. Alternatively spliced transcript variants encoding the same protein have been found for this gene.[provided by RefSeq, Dec 2010]

OMIM Research

OMIM ResearchGenerating clinical summary…

Active trials

Pubs (1 yr)

—

P/LP submissions

—

P/LP missense

1.44

LOEUF

Multiple*

Mechanism· predicted

Population Genetics & Constraint

gnomAD v4 — loss-of-function & missense intolerance

gnomAD

Tolerant — LoF & missense variants common in population

LoF Constraint?

1.44LOEUF

pLI 0.002

Z-score 0.76

OE 0.69 (0.36–1.44)

Tolerant

Highly tolerant — LoF variants common in population

Missense Constraint?

0.22Z-score

OE missense 0.93 (0.77–1.13)

74 obs / 79.6 exp

Tolerant

Mild missense constraint

Observed / Expected Ratios?

LoF OE?0.69 (0.36–1.44)

0≤0.351.4

Missense OE?0.93 (0.77–1.13)

0≤0.61.4

Synonymous OE?0.93

0≤1.21.6

LoF obs/exp: 5 / 7.2Missense obs/exp: 74 / 79.6Syn Z: 0.31

Background carrier burden — how many people carry a rare variant somewhere in CRABP2?

gnomAD v4 · ~731k individuals · PASS only

Rare means allele frequency under

Rare missense

1 in 340

164 rare PASS variants

Rare truncating (LoF)

1 in 1,300

40 rare PASS variants

Rare synonymous (reference)

1 in 520

82 rare PASS variants

Rare missense and truncating variants are carried at similar rates in CRABP2; this gene does not show strong loss-of-function constraint by this measure. 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 370	1 in 1,600
South Asian	~43k	1 in 220	≈ 1 in 11,000
Remaining (unassigned)	~30k	1 in 180	1 in 700
European (Finnish)	~27k	≈ 1 in 6,700	1 in 4,500
Admixed American	~22k	1 in 570	1 in 1,600
African / African American	~21k	1 in 290	1 in 2,200
East Asian	~20k	1 in 760	≈ 1 in 6,600
Ashkenazi Jewish	~13k	≈ 1 in 6,500	≈ 1 in 13,000
Middle Eastern	~2,884	1 in 410	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): All 4 coding exons well covered in gnomAD exomes and genomes.? see exons ↓