CLECL1P

C-type lectin like 1, pseudogene

Basic information

Region (hg38): 12:9722644-9733030

Previous symbols: [ "CLECL1" ]

Links

ENSG00000184293 ∙ NCBI:160365 ∙ OMIM:607467 ∙ HGNC:24462 ∙ Uniprot:Q8IZS7 ∙ 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 CLECL1P gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CLECL1P 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						0
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding			11	2		13
Total	0	0	11	2	0

Variants in CLECL1P

This is a list of pathogenic ClinVar variants found in the CLECL1P region.

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

Position	Type	Phenotype	Significance	ClinVar
12-9722722-C-G		not specified	Uncertain significance (Oct 12, 2021)
12-9722760-C-A		not specified	Likely benign (Sep 01, 2021)
12-9722760-C-T		not specified	Uncertain significance (Dec 17, 2023)
12-9722789-T-C		not specified	Uncertain significance (Dec 21, 2022)
12-9722789-T-G		not specified	Uncertain significance (Jun 13, 2024)
12-9732990-C-T		not specified	Uncertain significance (May 01, 2024)
12-9733008-G-A		not specified	Uncertain significance (Jan 22, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CLECL1P	protein_coding	protein_coding	ENST00000327839	2	17440

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.259	0.648	0	0	0	0	0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.170	83	87.5	0.949	0.00000425	1103
Missense in Polyphen		4	11.262	0.35517		169
Synonymous	0.0754	32	32.5	0.983	0.00000182	303
Loss of Function	1.24	1	3.51	0.285	1.46e-7	51

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.00	0.00
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May function in mediating immune cell-cell interactions. May act as a T-cell costimulatory molecule, enhancing anti-CD3- induced proliferation. May play a role in the interaction of dendritic cells with T-cells and the cells of the adaptive immune response. {ECO:0000269|PubMed:12421943}.

Intolerance Scores

• loftool: 0.809
• rvis_EVS: 0.62
• rvis_percentile_EVS: 83.14

Haploinsufficiency Scores

• pHI: 0.0466
• hipred: N
• hipred_score: 0.146

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.000413

Gene Damage Prediction

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

Gene ontology

• Biological process: positive regulation of T cell proliferation;interleukin-4 secretion;B cell adhesion
• Cellular component: plasma membrane;integral component of membrane
• Molecular function: molecular_function;carbohydrate binding