CRISP2

cysteine rich secretory protein 2, the group of Cysteine rich secretory protein family

Basic information

Region (hg38): 6:49692358-49713590

Previous symbols: [ "GAPDL5", "TPX1" ]

Links

ENSG00000124490 ∙ NCBI:7180 ∙ OMIM:187430 ∙ HGNC:12024 ∙ Uniprot:P16562 ∙ 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 CRISP2 gene.

• not_specified (28 variants)
• not_provided (3 variants)
• Megacolon (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CRISP2 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000003296.4. Only rare variants are included in the table.

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.

Effect	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous				1		1
missense			27	1		28
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			2			2
Total	0	0	29	2	0

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CRISP2	protein_coding	protein_coding	ENST00000339139	7	21202

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.44e-12	0.0143	125634	0	103	125737	0.000410

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.456	143	128	1.11	0.00000629	1591
Missense in Polyphen		59	51.783	1.1394		633
Synonymous	0.301	46	48.7	0.945	0.00000269	433
Loss of Function	-0.488	17	15.0	1.14	7.32e-7	173

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00340	0.00339
Ashkenazi Jewish	0.000809	0.000794
East Asian	0.000109	0.000109
Finnish	0.00	0.00
European (Non-Finnish)	0.000212	0.000211
Middle Eastern	0.000109	0.000109
South Asian	0.000165	0.000163
Other	0.000164	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May regulate some ion channels' activity and therebye regulate calcium fluxes during sperm capacitation. {ECO:0000250}.

Recessive Scores

• pRec: 0.0644

Intolerance Scores

• loftool: 0.984
• rvis_EVS: 0.95
• rvis_percentile_EVS: 90.01

Haploinsufficiency Scores

• pHI: 0.246
• hipred: N
• hipred_score: 0.112

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.254

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Crisp2

Gene ontology

• Cellular component: extracellular space