CRIP2

cysteine rich protein 2, the group of LIM domain containing

Basic information

Region (hg38): 14:105472962-105480162

Links

ENSG00000182809 ∙ NCBI:1397 ∙ OMIM:601183 ∙ HGNC:2361 ∙ Uniprot:P52943 ∙ 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 CRIP2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CRIP2 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				1	1	2
missense			15			15
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	1	1

Variants in CRIP2

This is a list of pathogenic ClinVar variants found in the CRIP2 region.

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

Position	Type	Phenotype	Significance	ClinVar
14-105473457-C-T			Likely benign (Feb 01, 2024)
14-105478469-G-A		not specified	Uncertain significance (Jul 14, 2023)
14-105478755-C-T		not specified	Uncertain significance (Sep 27, 2021)
14-105478775-C-A		not specified	Uncertain significance (Jul 11, 2023)
14-105478782-A-G		not specified	Uncertain significance (May 14, 2024)
14-105478788-C-A		not specified	Uncertain significance (Feb 12, 2024)
14-105478792-G-C		not specified	Uncertain significance (Sep 16, 2021)
14-105478798-C-T			Likely benign (Jun 18, 2018)
14-105478800-G-A		not specified	Uncertain significance (Jul 09, 2021)
14-105478821-C-G		not specified	Uncertain significance (Sep 12, 2023)
14-105478824-G-A		not specified	Uncertain significance (Jun 29, 2023)
14-105478832-G-A		not specified	Uncertain significance (Jan 24, 2023)
14-105478846-C-A		not specified	Uncertain significance (Sep 13, 2023)
14-105478865-A-C		not specified	Uncertain significance (Jun 24, 2022)
14-105479024-G-A		not specified	Uncertain significance (Feb 17, 2022)
14-105479046-C-A		not specified	Uncertain significance (May 03, 2023)
14-105479214-G-A		not specified	Uncertain significance (Jan 31, 2024)
14-105479441-C-T			Benign (Jun 18, 2018)
14-105479462-G-C		not specified	Uncertain significance (Feb 27, 2024)
14-105479615-A-G		not specified	Uncertain significance (Apr 17, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CRIP2	protein_coding	protein_coding	ENST00000483017	8	7201

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.000181	0.901	125119	0	12	125131	0.0000480

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.00456	159	159	0.999	0.00000957	1787
Missense in Polyphen		78	67.772	1.1509		707
Synonymous	-0.815	76	67.5	1.13	0.00000472	550
Loss of Function	1.50	8	14.1	0.569	6.70e-7	175

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000211	0.000186
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000544	0.0000544
Finnish	0.000139	0.000139
European (Non-Finnish)	0.0000474	0.0000443
Middle Eastern	0.0000544	0.0000544
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Recessive Scores

• pRec: 0.149

Haploinsufficiency Scores

• pHI: 0.253
• hipred: N
• hipred_score: 0.321
• ghis: 0.555

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.731

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Crip2
• Phenotype: behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); integument phenotype (the observable morphological and physiological characteristics of the skin and its associated structures, such as the hair, nails, sweat glands, sebaceous glands and other secretory glands that are manifested through development and lifespan)

Zebrafish Information Network

• Gene name: crip2
• Affected structure: atrioventricular ring
• Phenotype tag: abnormal
• Phenotype quality: aplastic

Gene ontology

• Biological process: positive regulation of cell population proliferation;hemopoiesis
• Cellular component: cell cortex
• Molecular function: protein binding;zinc ion binding