CRABP2
Basic information
Region (hg38): 1:156699606-156705816
Links
Phenotypes
GenCC
Source:
ClinVar
This is a list of variants' phenotypes submitted to
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the CRABP2 gene is commonly pathogenic or not.
In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.
Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.
| Variant type | Pathogenic | Likely pathogenic | VUS | Likely benign | Benign | Sum |
|---|---|---|---|---|---|---|
| synonymous | 0 | |||||
| missense | 10 | 10 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| inframe indel | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| splice region | 1 | 1 | ||||
| non coding | 0 | |||||
| Total | 0 | 0 | 10 | 0 | 0 |
Variants in CRABP2
This is a list of pathogenic ClinVar variants found in the CRABP2 region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
| Position | Type | Phenotype | Significance | ClinVar |
|---|---|---|---|---|
| 1-156700033-C-T | not specified | Uncertain significance (May 06, 2024) | ||
| 1-156700066-G-A | not specified | Uncertain significance (Nov 17, 2022) | ||
| 1-156700069-G-A | not specified | Uncertain significance (Oct 14, 2023) | ||
| 1-156700542-C-G | Likely benign (May 25, 2018) | |||
| 1-156700589-T-C | not specified | Uncertain significance (May 14, 2024) | ||
| 1-156700596-C-G | not specified | Uncertain significance (Aug 15, 2023) | ||
| 1-156700654-A-T | not specified | Uncertain significance (Jun 06, 2023) | ||
| 1-156700915-C-T | not specified | Uncertain significance (Dec 13, 2022) | ||
| 1-156700945-G-A | not specified | Uncertain significance (Sep 27, 2021) | ||
| 1-156700948-C-T | not specified | Uncertain significance (Sep 14, 2022) | ||
| 1-156701046-T-C | not specified | Uncertain significance (Feb 28, 2024) | ||
| 1-156701047-T-A | not specified | Uncertain significance (Oct 12, 2022) | ||
| 1-156705389-G-T | not specified | Uncertain significance (Oct 20, 2023) |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| CRABP2 | protein_coding | protein_coding | ENST00000368222 | 4 | 6211 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.00151 | 0.697 | 125666 | 0 | 82 | 125748 | 0.000326 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 0.224 | 74 | 79.6 | 0.929 | 0.00000433 | 903 |
| Missense in 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 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.000268 | 0.000268 |
| Ashkenazi Jewish | 0.00368 | 0.00368 |
| East Asian | 0.00 | 0.00 |
| Finnish | 0.0000463 | 0.0000462 |
| European (Non-Finnish) | 0.000282 | 0.000281 |
| Middle Eastern | 0.00 | 0.00 |
| South Asian | 0.00 | 0.00 |
| Other | 0.000817 | 0.000815 |
dbNSFP
Source:
- Function
- FUNCTION: Transports retinoic acid to the nucleus. Regulates the access of retinoic acid to the nuclear retinoic acid receptors.;
- Pathway
- Vitamin A and Carotenoid Metabolism;Signal Transduction;Signaling by Retinoic Acid;Signaling by Nuclear Receptors
(Consensus)
Recessive Scores
- pRec
- 0.198
Intolerance Scores
- loftool
- 0.545
- rvis_EVS
- -0.19
- rvis_percentile_EVS
- 39.68
Haploinsufficiency Scores
- pHI
- 0.783
- hipred
- Y
- hipred_score
- 0.607
- ghis
- 0.551
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.980
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Low | Medium |
| Primary Immunodeficiency | Medium | Low | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Crabp2
- Phenotype
- limbs/digits/tail phenotype; mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span);
Gene ontology
- Biological process
- retinoic acid biosynthetic process;regulation of transcription, DNA-templated;signal transduction;epidermis development;embryonic forelimb morphogenesis;regulation of retinoic acid receptor signaling pathway;positive regulation of collateral sprouting
- Cellular component
- nucleoplasm;endoplasmic reticulum;cytosol;extracellular exosome
- Molecular function
- retinoic acid binding;retinoid binding;protein binding;retinal binding;retinol binding