CRISPLD2

cysteine rich secretory protein LCCL domain containing 2

Basic information

Region (hg38): 16:84819984-84920768

Previous symbols: [ "LCRISP2" ]

Links

ENSG00000103196 ∙ NCBI:83716 ∙ OMIM:612434 ∙ HGNC:25248 ∙ Uniprot:Q9H0B8 ∙ 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 CRISPLD2 gene.

• Inborn genetic diseases (30 variants)
• not provided (12 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CRISPLD2 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				2	3	5
missense			30	2	3	35
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region					1	1
non coding					1	1
Total	0	0	30	4	7

Variants in CRISPLD2

This is a list of pathogenic ClinVar variants found in the CRISPLD2 region.

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

Position	Type	Phenotype	Significance	ClinVar
16-84838545-T-G		not specified	Uncertain significance (Oct 26, 2021)
16-84838560-G-A		CRISPLD2-related disorder	Likely benign (Jul 18, 2022)
16-84838576-C-T		CRISPLD2-related disorder	Likely benign (Jul 11, 2019)
16-84838598-C-T		not specified	Uncertain significance (Apr 06, 2023)
16-84838653-G-C		not specified	Uncertain significance (Dec 12, 2023)
16-84838658-G-T		not specified	Uncertain significance (Jun 02, 2023)
16-84838697-G-A		not specified	Uncertain significance (Jan 04, 2022)
16-84838702-G-T		CRISPLD2-related disorder	Uncertain significance (Dec 27, 2023)
16-84838721-A-G		not specified	Uncertain significance (Jun 21, 2023)
16-84845825-G-C		not specified	Uncertain significance (Oct 06, 2022)
16-84845851-G-A		CRISPLD2-related disorder	Likely benign (Aug 21, 2022)
16-84845886-T-C		not specified	Uncertain significance (Feb 27, 2024)
16-84845891-G-A		not specified	Uncertain significance (Nov 01, 2022)
16-84845894-C-T		not specified	Uncertain significance (May 18, 2023)
16-84849378-C-T		CRISPLD2-related disorder	Likely benign (Jun 21, 2023)
16-84849390-G-A		not specified	Uncertain significance (Apr 25, 2023)
16-84849391-C-T		CRISPLD2-related disorder	Likely benign (Jul 16, 2019)
16-84849395-C-G		not specified	Uncertain significance (Feb 06, 2024)
16-84849397-G-C		CRISPLD2-related disorder	Likely benign (Jul 09, 2019)
16-84849447-C-T		not specified	Uncertain significance (Aug 02, 2021)
16-84849457-C-A		CRISPLD2-related disorder	Likely benign (Jun 19, 2019)
16-84849471-G-C		not specified	Uncertain significance (Jan 07, 2022)
16-84849491-G-A		not specified	Uncertain significance (Mar 29, 2022)
16-84850594-C-T		CRISPLD2-related disorder	Benign (Jun 07, 2019)
16-84850611-C-G		not specified	Uncertain significance (Apr 07, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CRISPLD2	protein_coding	protein_coding	ENST00000262424	14	100785

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
7.82e-9	0.975	125674	0	73	125747	0.000290

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-1.60	390	311	1.26	0.0000190	3252
Missense in Polyphen		148	142.13	1.0413		1409
Synonymous	-2.47	167	131	1.27	0.00000970	917
Loss of Function	2.17	18	31.1	0.579	0.00000141	356

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000641	0.000612
Ashkenazi Jewish	0.00	0.00
East Asian	0.000109	0.000109
Finnish	0.000257	0.000231
European (Non-Finnish)	0.000401	0.000378
Middle Eastern	0.000109	0.000109
South Asian	0.000230	0.000229
Other	0.000353	0.000326

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Promotes matrix assembly. {ECO:0000250}.
• Pathway: Neutrophil degranulation;Innate Immune System;Immune System (Consensus)

Recessive Scores

• pRec: 0.106

Intolerance Scores

• loftool: 0.235
• rvis_EVS: 0.45
• rvis_percentile_EVS: 78

Haploinsufficiency Scores

• pHI: 0.777
• hipred: N
• hipred_score: 0.229
• ghis: 0.498

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.185

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Crispld2
• Phenotype: skeleton phenotype; immune system phenotype; embryo phenotype; growth/size/body region phenotype; mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); homeostasis/metabolism phenotype

Zebrafish Information Network

• Gene name: crispld2
• Affected structure: hypophyseal fenestra
• Phenotype tag: abnormal
• Phenotype quality: decreased size

Gene ontology

• Biological process: extracellular matrix organization;lung development;neutrophil degranulation;face morphogenesis
• Cellular component: extracellular region;extracellular space;transport vesicle;extracellular matrix;secretory granule lumen;extracellular exosome;ficolin-1-rich granule lumen
• Molecular function: glycosaminoglycan binding;heparin binding