CRISPLD1

cysteine rich secretory protein LCCL domain containing 1

Basic information

Region (hg38): 8:74984504-75034558

Previous symbols: [ "LCRISP1" ]

Links

ENSG00000121005 ∙ NCBI:83690 ∙ ∙ HGNC:18206 ∙ Uniprot:Q9H336 ∙ 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 CRISPLD1 gene.

• Inborn genetic diseases (21 variants)
• not provided (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CRISPLD1 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			20	1		21
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region					1	1
non coding						0
Total	0	0	20	1	0

Variants in CRISPLD1

This is a list of pathogenic ClinVar variants found in the CRISPLD1 region.

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

Position	Type	Phenotype	Significance	ClinVar
8-74986036-A-G		not specified	Uncertain significance (Nov 03, 2022)
8-74986042-A-G		not specified	Uncertain significance (Jun 21, 2023)
8-74986046-C-T		not specified	Uncertain significance (Sep 26, 2023)
8-74986094-T-G		not specified	Uncertain significance (Apr 06, 2023)
8-74986193-A-G		not specified	Uncertain significance (Sep 22, 2023)
8-74986213-G-T		not specified	Uncertain significance (Sep 20, 2023)
8-74986222-A-G		not specified	Uncertain significance (Mar 01, 2024)
8-75012441-T-A		not specified	Uncertain significance (Dec 08, 2023)
8-75012497-G-C		not specified	Uncertain significance (Apr 20, 2023)
8-75012901-C-T		not specified	Uncertain significance (Aug 09, 2021)
8-75012954-T-C		not specified	Uncertain significance (Sep 27, 2022)
8-75013990-G-A		not specified	Uncertain significance (Jun 07, 2023)
8-75013999-A-G		not specified	Uncertain significance (Dec 19, 2022)
8-75016580-A-G		not specified	Uncertain significance (Dec 21, 2023)
8-75016652-G-A		not specified	Likely benign (Jul 27, 2022)
8-75016712-C-A			Benign (Jun 09, 2018)
8-75016914-A-T		not specified	Uncertain significance (Apr 12, 2022)
8-75016915-T-A		not specified	Uncertain significance (Oct 27, 2022)
8-75016919-T-C		not specified	Uncertain significance (Dec 17, 2021)
8-75016926-G-A		not specified	Uncertain significance (Jun 26, 2023)
8-75017341-G-T		not specified	Uncertain significance (Jul 11, 2023)
8-75017344-A-G		not specified	Uncertain significance (Sep 27, 2021)
8-75017426-A-G		not specified	Uncertain significance (Oct 10, 2023)
8-75020064-C-T		not specified	Uncertain significance (Aug 21, 2023)
8-75020070-A-G		not specified	Uncertain significance (Nov 30, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CRISPLD1	protein_coding	protein_coding	ENST00000262207	14	50044

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.82e-9	0.991	125674	0	73	125747	0.000290

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.487	251	274	0.917	0.0000136	3279
Missense in Polyphen		76	89.354	0.85055		1102
Synonymous	1.30	76	91.9	0.827	0.00000475	894
Loss of Function	2.47	20	36.0	0.556	0.00000202	392

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000211	0.000210
Ashkenazi Jewish	0.00	0.00
East Asian	0.00258	0.00256
Finnish	0.00	0.00
European (Non-Finnish)	0.000142	0.000141
Middle Eastern	0.00258	0.00256
South Asian	0.000141	0.000131
Other	0.000163	0.000163

dbNSFP

Source: dbNSFP

Recessive Scores

• pRec: 0.101

Intolerance Scores

• loftool: 0.469
• rvis_EVS: -0.56
• rvis_percentile_EVS: 19.54

Haploinsufficiency Scores

• pHI: 0.394
• hipred: Y
• hipred_score: 0.540
• ghis: 0.553

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.106

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Crispld1

Gene ontology

• Biological process: face morphogenesis
• Cellular component: extracellular space;extracellular exosome
• Molecular function: molecular_function