CLPSL2

colipase like 2

Basic information

Region (hg38): 6:35776594-35779552

Previous symbols: [ "C6orf126" ]

Links

ENSG00000196748 ∙ NCBI:389383 ∙ ∙ HGNC:21250 ∙ Uniprot:Q6UWE3 ∙ 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 CLPSL2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CLPSL2 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			6			6
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	6	0	0

Variants in CLPSL2

This is a list of pathogenic ClinVar variants found in the CLPSL2 region.

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

Position	Type	Phenotype	Significance	ClinVar
6-35776673-C-T		not specified	Uncertain significance (Dec 02, 2022)
6-35777480-C-T		not specified	Uncertain significance (May 29, 2024)
6-35777498-A-G		not specified	Uncertain significance (Mar 24, 2023)
6-35779371-A-G		not specified	Uncertain significance (May 23, 2023)
6-35779388-C-T		not specified	Uncertain significance (Jun 21, 2021)
6-35779401-C-T		not specified	Uncertain significance (May 04, 2022)
6-35779430-C-T		not specified	Uncertain significance (Mar 29, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CLPSL2	protein_coding	protein_coding	ENST00000403376	3	2959

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.186	0.658	125455	0	19	125474	0.0000757

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.422	42	50.4	0.833	0.00000252	636
Missense in Polyphen		13	15.661	0.83011		160
Synonymous	-0.282	21	19.4	1.08	0.00000105	192
Loss of Function	0.911	1	2.58	0.388	1.09e-7	40

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000264	0.000264
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000974	0.0000970
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Intolerance Scores

• rvis_EVS: 0.32
• rvis_percentile_EVS: 72.94

Haploinsufficiency Scores

• pHI: 0.0884
• hipred: N
• hipred_score: 0.123

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.114

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Clpsl2

Gene ontology

• Biological process: digestion;lipid catabolic process;response to food;positive regulation of catalytic activity
• Cellular component: extracellular region
• Molecular function: enzyme activator activity