CRABP2

protein-coding

cellular retinoic acid binding protein 2, the group of Fatty acid binding protein family

Gene summary

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]

MANE transcript

NM_001878.4

Inheritance

—

ClinVar variants

U:24B:2

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.69

Max pathogenic AF

—

Genomic locus

chr1:156,699,606-156,705,816

External References & Databases

Ensembl (ENSG00000143320)

Transcript & Mutation Effects

hg38 • Region Span ~6.2 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to CRABP2 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 22

not providedTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_001878.4. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous			1 clinvar	1 clinvar		2
missense			22 clinvar	1 clinvar		23
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			1 clinvar			1
Total	0	0	24	2	0	26

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 31 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_001878.4	RefSeq	NP_001869.1	4	MANE Select
ENST00000368222.8	Ensembl	ENSP00000357205.3	4	MANE Select
NM_001199723.2	RefSeq	NP_001186652.1	4	Standard
ENST00000368220.1	Ensembl	ENSP00000357203.1	2	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

Vitamin A and Carotenoid Metabolism
Signal Transduction
Signaling by Retinoic Acid
Signaling by Nuclear Receptors

Biological Process

retinoic acid biosynthetic process
regulation of transcription, DNA-templated
signal transduction
epidermis development
embryonic forelimb morphogenesis

Molecular Function

retinoic acid binding
retinoid binding
protein binding
retinal binding
retinol binding

Cellular Component

nucleoplasm
endoplasmic reticulum
cytosol
extracellular exosome

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000368222
Coding exons: 4
Length: 6211
Individuals with no LoFs: 125666
Homozygous LoFs: 0
Heterozygous LoFs: 82
Defined: 125748
p: 0.000326

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.224	74	79.6	0.929	0.00000433	903
Missense (PolyPhen)		15	16.215	0.92508		201
Synonymous	0.309	32	34.3	0.933	0.00000224	261
Loss of Function	0.758	5	7.19	0.695	3.09e-7	84

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00012	0.00012	rare
Latino/Admixed American	0.00014	0.00014	rare
Ashkenazi Jewish	0.0037	0.0037	notable
East Asian	0	0.0	absent
Finnish	0.000046	0.000046	rare
European (Non-Finnish)	0.00028	0.00028	rare
South Asian	0	0.0	absent
Other	0.00082	0.00081	rare

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: Transports retinoic acid to the nucleus. Regulates the access of retinoic acid to the nuclear retinoic acid receptors.;

Recessive Scores

pRec: 0.198

Intolerance Scores

LoFtool: 0.545
RVIS EVS: -0.19
RVIS percentile EVS: 39.68

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: E
Indispensability score: 0.980

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Low	Medium
Primary Immunodeficiency	Medium	Low	Medium
Cancer	Medium	Medium	Medium