CRISP3

cysteine rich secretory protein 3, the group of Cysteine rich secretory protein family

Basic information

Region (hg38): 6:49727376-49744437

Links

ENSG00000096006 ∙ NCBI:10321 ∙ OMIM:618062 ∙ HGNC:16904 ∙ Uniprot:P54108 ∙ 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 CRISP3 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CRISP3 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			14	1		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	14	1	0

Variants in CRISP3

This is a list of pathogenic ClinVar variants found in the CRISP3 region.

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

Position	Type	Phenotype	Significance	ClinVar
6-49728753-T-G		not specified	Uncertain significance (Jul 19, 2022)
6-49728777-T-C		not specified	Uncertain significance (Jan 20, 2025)
6-49728782-A-C		not specified	Uncertain significance (Dec 25, 2024)
6-49728848-C-T		not specified	Uncertain significance (Jan 24, 2024)
6-49731175-C-T		not specified	Likely benign (Dec 25, 2024)
6-49731189-G-A		not specified	Uncertain significance (Nov 21, 2022)
6-49731219-T-A		not specified	Uncertain significance (Sep 08, 2024)
6-49731223-G-T		not specified	Uncertain significance (Aug 21, 2023)
6-49733243-G-A		not specified	Uncertain significance (Jan 28, 2025)
6-49733252-G-A		not specified	Uncertain significance (Jun 22, 2023)
6-49733267-A-G		not specified	Uncertain significance (Apr 19, 2023)
6-49733268-C-T		not specified	Uncertain significance (May 26, 2022)
6-49733720-C-T		not specified	Uncertain significance (Mar 28, 2024)
6-49733762-C-T		not specified	Uncertain significance (Mar 21, 2022)
6-49733764-T-C		not specified	Uncertain significance (Dec 22, 2024)
6-49733792-C-T		not specified	Uncertain significance (May 21, 2024)
6-49735557-T-C		not specified	Uncertain significance (Feb 23, 2025)
6-49735584-T-C		not specified	Likely benign (Aug 15, 2023)
6-49736501-C-A		not specified	Uncertain significance (Mar 07, 2025)
6-49737344-A-G		not specified	Uncertain significance (Jan 21, 2025)
6-49737362-G-A		not specified	Uncertain significance (Oct 26, 2021)
6-49737394-C-T		not specified	Uncertain significance (Oct 26, 2021)
6-49744333-G-C		not specified	Uncertain significance (Jan 17, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CRISP3	protein_coding	protein_coding	ENST00000433368	8	17054

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00000257	0.759	125650	0	54	125704	0.000215

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.379	150	138	1.09	0.00000637	1758
Missense in Polyphen		31	38.448	0.80628		490
Synonymous	-0.981	60	51.1	1.17	0.00000271	470
Loss of Function	1.23	11	16.4	0.672	8.54e-7	181

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000221	0.000221
Ashkenazi Jewish	0.000216	0.000198
East Asian	0.0000546	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.000398	0.000396
Middle Eastern	0.0000546	0.0000544
South Asian	0.00	0.00
Other	0.000163	0.000163

dbNSFP

Source: dbNSFP

• Pathway: Neutrophil degranulation;Innate Immune System;Immune System (Consensus)

Recessive Scores

• pRec: 0.127

Intolerance Scores

• loftool: 0.921
• rvis_EVS: 0.13
• rvis_percentile_EVS: 63.2

Haploinsufficiency Scores

• pHI: 0.0949
• hipred: N
• hipred_score: 0.112
• ghis: 0.379

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.523

Gene Damage Prediction

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

Gene ontology

• Biological process: defense response;neutrophil degranulation;innate immune response
• Cellular component: extracellular region;extracellular space;extracellular matrix;specific granule lumen;specific granule;tertiary granule lumen
• Molecular function: molecular_function