CILP2

cartilage intermediate layer protein 2, the group of Immunoglobulin like domain containing

Basic information

Region (hg38): 19:19538247-19546659

Links

ENSG00000160161 ∙ NCBI:148113 ∙ OMIM:612419 ∙ HGNC:24213 ∙ Uniprot:Q8IUL8 ∙ 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 CILP2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CILP2 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			87	5		92
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	87	5	0

Variants in CILP2

This is a list of pathogenic ClinVar variants found in the CILP2 region.

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

Position	Type	Phenotype	Significance	ClinVar
19-19539680-C-A		not specified	Uncertain significance (Jun 23, 2023)
19-19540206-G-A		not specified	Uncertain significance (Feb 17, 2023)
19-19540212-G-C		not specified	Uncertain significance (Sep 13, 2023)
19-19540232-C-A		not specified	Uncertain significance (Oct 29, 2021)
19-19540249-G-A		not specified	Uncertain significance (Apr 22, 2024)
19-19540260-T-A		not specified	Uncertain significance (Apr 15, 2024)
19-19540281-C-A		not specified	Uncertain significance (Oct 29, 2021)
19-19540302-C-T		not specified	Uncertain significance (Dec 21, 2023)
19-19540365-G-A		not specified	Uncertain significance (Feb 06, 2024)
19-19540464-C-G		not specified	Uncertain significance (Aug 04, 2023)
19-19541175-C-T		not specified	Uncertain significance (Feb 07, 2023)
19-19541201-G-T		not specified	Uncertain significance (Mar 17, 2023)
19-19541217-C-A		not specified	Uncertain significance (Jul 26, 2023)
19-19542497-A-G		not specified	Uncertain significance (Feb 15, 2023)
19-19542503-G-A		not specified	Uncertain significance (Oct 06, 2021)
19-19542522-G-A		not specified	Likely benign (Jan 10, 2023)
19-19542548-C-T		not specified	Uncertain significance (Jan 09, 2024)
19-19542549-G-A		not specified	Likely benign (Jan 02, 2024)
19-19542593-G-A		not specified	Uncertain significance (Feb 06, 2024)
19-19542597-A-C		not specified	Uncertain significance (May 24, 2023)
19-19542611-G-A		not specified	Uncertain significance (Mar 28, 2024)
19-19542886-C-A		not specified	Uncertain significance (May 31, 2023)
19-19542897-G-C		not specified	Uncertain significance (Mar 06, 2023)
19-19542908-G-T		not specified	Uncertain significance (Apr 12, 2024)
19-19542939-C-T		not specified	Uncertain significance (Dec 05, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CILP2	protein_coding	protein_coding	ENST00000291495	8	8412

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
8.03e-8	0.999	125673	0	75	125748	0.000298

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.881	699	768	0.911	0.0000552	7214
Missense in Polyphen		238	288.97	0.82361		2823
Synonymous	1.79	302	344	0.877	0.0000258	2564
Loss of Function	2.92	18	37.2	0.483	0.00000230	361

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000663	0.000652
Ashkenazi Jewish	0.000199	0.000198
East Asian	0.000228	0.000217
Finnish	0.0000468	0.0000462
European (Non-Finnish)	0.000271	0.000264
Middle Eastern	0.000228	0.000217
South Asian	0.000528	0.000523
Other	0.000499	0.000489

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May play a role in cartilage scaffolding. {ECO:0000250|UniProtKB:O75339}.

Recessive Scores

• pRec: 0.111

Intolerance Scores

• loftool: 0.643
• rvis_EVS: -1.08
• rvis_percentile_EVS: 7.24

Haploinsufficiency Scores

• pHI: 0.163
• hipred: Y
• hipred_score: 0.667
• ghis: 0.445

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.220

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Cilp2

Gene ontology

• Biological process: dephosphorylation
• Cellular component: extracellular exosome
• Molecular function: alkaline phosphatase activity;nucleotide diphosphatase activity