CILP

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

Basic information

Region (hg38): 15:65194759-65211473

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.

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.

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				6	1	7
missense			89	2	6	97
nonsense			1			1
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	90	8	7

Variants in CILP

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

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

Position	Type	Phenotype	Significance	ClinVar
15-65196790-C-T		CILP-related disorder	Benign (Oct 16, 2019)
15-65196835-G-T		not specified	Uncertain significance (Dec 13, 2021)
15-65196910-G-A		not specified	Uncertain significance (Apr 05, 2023)
15-65196919-G-C		not specified	Uncertain significance (Feb 13, 2024)
15-65196945-G-C		not specified	Uncertain significance (Sep 01, 2021)
15-65196948-A-G			Uncertain significance (-)
15-65197052-A-G		CILP-related disorder	Likely benign (May 24, 2019)
15-65197062-C-T		not specified	Uncertain significance (May 31, 2023)
15-65197096-G-A			Benign (Aug 03, 2017)
15-65197117-C-T		not specified	Uncertain significance (Nov 21, 2022)
15-65197185-C-T		not specified	Likely benign (Aug 22, 2023)
15-65197186-G-A		not specified	Uncertain significance (Jan 08, 2024)
15-65197231-G-A		not specified	Uncertain significance (Dec 02, 2022)
15-65197231-G-C		not specified	Uncertain significance (Mar 04, 2024)
15-65197251-C-T		not specified	Uncertain significance (May 26, 2024)
15-65197278-G-T		not specified	Uncertain significance (Jun 22, 2023)
15-65197305-C-T		not specified	Uncertain significance (Nov 18, 2022)
15-65197306-G-A		not specified	Uncertain significance (Dec 04, 2023)
15-65197345-C-T		not specified	Uncertain significance (Jul 17, 2023)
15-65197350-T-C		CILP-related disorder	Benign (Jan 02, 2020)
15-65197367-C-T		not specified	Uncertain significance (May 27, 2022)
15-65197479-C-T		not specified	Uncertain significance (Feb 06, 2023)
15-65197527-T-C			Uncertain significance (-)
15-65197588-G-A		not specified	Uncertain significance (Mar 06, 2023)
15-65197693-C-T		not specified	Uncertain significance (Jan 31, 2024)

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

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