CRIP3

cysteine rich protein 3, the group of LIM domain containing

Basic information

Region (hg38): 6:43299710-43308826

Links

ENSG00000146215 ∙ NCBI:401262 ∙ ∙ HGNC:17751 ∙ Uniprot:Q6Q6R5 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the CRIP3 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CRIP3 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			12			12
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	12	0	0

Variants in CRIP3

This is a list of pathogenic ClinVar variants found in the CRIP3 region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
6-43299928-C-T		not specified	Uncertain significance (Dec 19, 2022)
6-43299946-G-A		not specified	Uncertain significance (Jun 30, 2022)
6-43299970-T-G		not specified	Uncertain significance (Oct 05, 2023)
6-43299988-T-C		not specified	Uncertain significance (Apr 13, 2022)
6-43300002-C-T		not specified	Uncertain significance (May 31, 2022)
6-43300051-G-A		not specified	Uncertain significance (May 15, 2023)
6-43301212-C-T		not specified	Uncertain significance (Aug 23, 2021)
6-43301596-T-C		not specified	Uncertain significance (Mar 29, 2023)
6-43301601-G-A		not specified	Uncertain significance (Feb 22, 2024)
6-43301655-C-T		not specified	Uncertain significance (Dec 01, 2022)
6-43301682-G-A		not specified	Likely benign (Aug 15, 2023)
6-43302285-G-A		not specified	Uncertain significance (Jul 05, 2022)
6-43302390-G-A		not specified	Uncertain significance (Feb 15, 2023)
6-43302689-G-A		not specified	Uncertain significance (Oct 16, 2023)
6-43304100-C-A		not specified	Uncertain significance (Sep 16, 2021)
6-43304115-G-A		not specified	Uncertain significance (Nov 09, 2023)
6-43304127-C-T		not specified	Uncertain significance (Sep 15, 2021)
6-43304156-G-A		not specified	Uncertain significance (Jun 19, 2024)
6-43304187-T-G		not specified	Uncertain significance (Apr 07, 2022)
6-43304703-C-T		not specified	Uncertain significance (Feb 28, 2024)
6-43306232-C-T		not specified	Uncertain significance (Apr 20, 2023)
6-43306253-C-A		not specified	Uncertain significance (Sep 15, 2021)
6-43306277-C-T		not specified	Uncertain significance (Mar 08, 2024)
6-43306517-C-T		not specified	Uncertain significance (Apr 13, 2023)
6-43307660-T-C		not specified	Uncertain significance (Nov 18, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CRIP3	protein_coding	protein_coding	ENST00000372569	8	9088

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.000648	0.918	125555	0	190	125745	0.000756

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.0639	114	116	0.983	0.00000594	1333
Missense in Polyphen		52	50.946	1.0207		581
Synonymous	-0.357	49	45.9	1.07	0.00000259	389
Loss of Function	1.55	7	13.0	0.538	6.38e-7	151

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000305	0.000304
Ashkenazi Jewish	0.00	0.00
East Asian	0.00343	0.00343
Finnish	0.000374	0.000370
European (Non-Finnish)	0.000863	0.000844
Middle Eastern	0.00343	0.00343
South Asian	0.000425	0.000425
Other	0.000496	0.000489

dbNSFP

Source: dbNSFP

Recessive Scores

• pRec: 0.107

Intolerance Scores

• loftool: 0.507
• rvis_EVS: -0.07
• rvis_percentile_EVS: 48.12

Haploinsufficiency Scores

• pHI: 0.182
• hipred: N
• hipred_score: 0.310
• ghis: 0.517

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.116

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Crip3
• Phenotype: endocrine/exocrine gland phenotype; immune system phenotype; hematopoietic system phenotype

Gene ontology

• Cellular component: cytoplasm
• Molecular function: metal ion binding