CILP

cartilage intermediate layer protein, the group of Immunoglobulin like domain containing

Basic information

Region (hg38): 15:65194760-65211473

Links

ENSG00000138615

∙ NCBI:8483 ∙ OMIM:603489 ∙ HGNC:1980 ∙ Uniprot:O75339 ∙ 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 CILP gene.

not_specified (196 variants)
CILP-related_disorder (7 variants)
not_provided (6 variants)
See_cases (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CILP gene is commonly pathogenic or not. These statistics are base on transcript: NM_000003613.4. 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	PathogenicP	Likely pathogenicLP	VUSVUS	Likely benignLB	BenignB	Sum
synonymous				6 clinvar	1 clinvar	7
missense			189 clinvar	8 clinvar	3 clinvar	200
nonsense			1 clinvar			1
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	190	14	4

Loading clinvar variants...

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CILP	protein_coding	protein_coding	ENST00000261883	8	15490

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
5.37e-26	0.000323	125492	3	253	125748	0.00102

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.170	693	706	0.982	0.0000418	7772
Missense in Polyphen		332	339.52	0.97786		3706
Synonymous	0.573	258	270	0.956	0.0000147	2404
Loss of Function	0.0626	39	39.4	0.989	0.00000215	451

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00256	0.00255
Ashkenazi Jewish	0.000198	0.000198
East Asian	0.00191	0.00180
Finnish	0.000372	0.000370
European (Non-Finnish)	0.000795	0.000783
Middle Eastern	0.00191	0.00180
South Asian	0.00184	0.00170
Other	0.00213	0.00212

dbNSFP

Source: dbNSFP

Function: FUNCTION: Probably plays a role in cartilage scaffolding. May act by antagonizing TGF-beta1 (TGFB1) and IGF1 functions. Has the ability to suppress IGF1-induced proliferation and sulfated proteoglycan synthesis, and inhibits ligand-induced IGF1R autophosphorylation. May inhibit TGFB1-mediated induction of cartilage matrix genes via its interaction with TGFB1. Overexpression may lead to impair chondrocyte growth and matrix repair and indirectly promote inorganic pyrophosphate (PPi) supersaturation in aging and osteoarthritis cartilage. {ECO:0000269|PubMed:12746903, ECO:0000269|PubMed:15864306}.;
Disease: DISEASE: Intervertebral disc disease (IDD) [MIM:603932]: A common musculo-skeletal disorder caused by degeneration of intervertebral disks of the lumbar spine. It results in low-back pain and unilateral leg pain. {ECO:0000269|PubMed:15864306}. Note=Disease susceptibility is associated with variations affecting the gene represented in this entry. {ECO:0000269|PubMed:15864306}.;
Pathway: Signal Transduction;Signaling by Receptor Tyrosine Kinases;Signaling by Type 1 Insulin-like Growth Factor 1 Receptor (IGF1R) (Consensus)

Recessive Scores

pRec: 0.139

Intolerance Scores

loftool: 0.980
rvis_EVS: -1.53
rvis_percentile_EVS: 3.34

Haploinsufficiency Scores

pHI: 0.251
hipred: N
hipred_score: 0.216
ghis: 0.529

Essentials

essential_gene_CRISPR: N
essential_gene_CRISPR2: N
essential_gene_gene_trap: N
gene_indispensability_pred: N
gene_indispensability_score: 0.376

Gene Damage Prediction

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

Mouse Genome Informatics

Gene name: Cilp
Phenotype

Gene ontology

Biological process: negative regulation of gene expression;dephosphorylation;negative regulation of insulin-like growth factor receptor signaling pathway;negative regulation of SMAD protein signal transduction;cellular response to transforming growth factor beta stimulus
Cellular component: extracellular space;collagen-containing extracellular matrix;extracellular exosome
Molecular function: alkaline phosphatase activity;nucleotide diphosphatase activity;extracellular matrix structural constituent