CRIP1

cysteine rich protein 1, the group of LIM domain containing

Basic information

Region (hg38): 14:105486317-105488947

Links

ENSG00000213145 ∙ NCBI:1396 ∙ OMIM:123875 ∙ HGNC:2360 ∙ Uniprot:P50238 ∙ 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 CRIP1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CRIP1 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			15		1	16
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	15	0	1

Variants in CRIP1

This is a list of pathogenic ClinVar variants found in the CRIP1 region.

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

Position	Type	Phenotype	Significance	ClinVar
14-105487290-G-C		not specified	Uncertain significance (Oct 06, 2022)
14-105488172-G-C		not specified	Uncertain significance (Oct 28, 2024)
14-105488186-G-T		not specified	Uncertain significance (Nov 29, 2023)
14-105488201-C-T		not specified	Uncertain significance (Jan 27, 2025)
14-105488202-G-A		not specified	Uncertain significance (Jun 18, 2021)
14-105488209-C-G		not specified	Uncertain significance (Jan 30, 2024)
14-105488214-A-G		not specified	Uncertain significance (Oct 27, 2022)
14-105488225-T-C		not specified	Uncertain significance (Nov 14, 2024)
14-105488235-C-T		not specified	Uncertain significance (Dec 12, 2024)
14-105488238-T-C		not specified	Uncertain significance (Jun 13, 2023)
14-105488334-G-A		not specified	Uncertain significance (Dec 31, 2023)
14-105488350-G-T			Benign (May 30, 2017)
14-105488359-C-A		not specified	Uncertain significance (Apr 08, 2024)
14-105488473-T-C		not specified	Uncertain significance (Aug 20, 2024)
14-105488479-C-G		not specified	Uncertain significance (Jun 16, 2023)
14-105488480-G-A		not specified	Uncertain significance (Jan 30, 2025)
14-105488480-G-C		not specified	Uncertain significance (Jan 30, 2024)
14-105488491-G-A		not specified	Uncertain significance (Mar 17, 2023)
14-105488505-C-G		not specified	Uncertain significance (Jan 09, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CRIP1	protein_coding	protein_coding	ENST00000330233	4	2631

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.000498	0.460	125332	0	23	125355	0.0000917

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.734	61	46.9	1.30	0.00000286	487
Missense in Polyphen		17	11.469	1.4823		150
Synonymous	-0.0216	19	18.9	1.01	0.00000137	133
Loss of Function	0.137	5	5.34	0.936	2.26e-7	67

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000289	0.0000289
Ashkenazi Jewish	0.00	0.00
East Asian	0.000436	0.000435
Finnish	0.0000469	0.0000462
European (Non-Finnish)	0.0000623	0.0000619
Middle Eastern	0.000436	0.000435
South Asian	0.000198	0.000196
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Seems to have a role in zinc absorption and may function as an intracellular zinc transport protein.

Recessive Scores

• pRec: 0.113

Intolerance Scores

• loftool: 0.576
• rvis_EVS: 0.28
• rvis_percentile_EVS: 71.08

Haploinsufficiency Scores

• pHI: 0.166
• hipred: N
• hipred_score: 0.146
• ghis: 0.409

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.994

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Crip1

Zebrafish Information Network

• Gene name: crip1
• Affected structure: trunk
• Phenotype tag: abnormal
• Phenotype quality: curved dorsal

Gene ontology

• Biological process: immune response;heart development;cell population proliferation;intrinsic apoptotic signaling pathway in response to DNA damage;response to organic substance;response to zinc ion;regulation of gene expression;prostate gland stromal morphogenesis;cellular response to antibiotic;cellular response to UV-B
• Cellular component: cytoplasm
• Molecular function: AT DNA binding;zinc ion binding;DNA binding, bending;peptide binding