GeneBe

CRISPLD2

cysteine rich secretory protein LCCL domain containing 2

Basic information

Region (hg38): 16:84819985-84920768

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.

  • not_specified (105 variants)
  • CRISPLD2-related_disorder (31 variants)
  • not_provided (11 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. These statistics are base on transcript: NM_000031476.4. 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.

EffectPLPVUSLBBSum
synonymous
10
clinvar
5
clinvar
 15
missense
105
clinvar
5
clinvar
3
clinvar
 113
nonsense
0
start loss
0
frameshift
0
splice donor/acceptor (+/-2bp)
0
Total 0 0 105 15 8
Loading clinvar variants...

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
CRISPLD2protein_codingprotein_codingENST00000262424 14100785
pLI Probability
LOF Intolerant 		pRec Probability
LOF Recessive 		Individuals with
no LOFs 		Individuals with
Homozygous LOFs 		Individuals with
Heterozygous LOFs 		Defined p
7.82e-90.9751256740731257470.000290
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense-1.603903111.260.00001903252
Missense in Polyphen148142.131.04131409
Synonymous-2.471671311.270.00000970917
Loss of Function2.171831.10.5790.00000141356

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.0006410.000612
Ashkenazi Jewish0.000.00
East Asian0.0001090.000109
Finnish0.0002570.000231
European (Non-Finnish)0.0004010.000378
Middle Eastern0.0001090.000109
South Asian0.0002300.000229
Other0.0003530.000326

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

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyHighMediumHigh
CancerHighMediumHigh

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