CLPSL1

colipase like 1

Basic information

Region (hg38): 6:35781019-35793675

Previous symbols: [ "C6orf127" ]

Links

ENSG00000204140 ∙ NCBI:340204 ∙ ∙ HGNC:21251 ∙ Uniprot:A2RUU4 ∙ 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 CLPSL1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CLPSL1 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			17	1		18
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	17	1	0

Variants in CLPSL1

This is a list of pathogenic ClinVar variants found in the CLPSL1 region.

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

Position	Type	Phenotype	Significance	ClinVar
6-35781139-T-C		not specified	Uncertain significance (Sep 08, 2024)
6-35781178-G-A		not specified	Uncertain significance (Jan 24, 2024)
6-35787000-G-C		not specified	Likely benign (Aug 20, 2024)
6-35787008-A-G		not specified	Uncertain significance (Jan 17, 2024)
6-35787020-G-C		not specified	Uncertain significance (Nov 08, 2021)
6-35787046-T-C		not specified	Uncertain significance (Nov 15, 2024)
6-35787055-G-A		not specified	Uncertain significance (Dec 09, 2023)
6-35787058-C-G		not specified	Uncertain significance (Feb 15, 2023)
6-35787078-C-G		not specified	Uncertain significance (Nov 22, 2024)
6-35787079-T-G		not specified	Uncertain significance (May 02, 2024)
6-35787867-G-A		not specified	Uncertain significance (Dec 12, 2023)
6-35787877-G-A		not specified	Uncertain significance (Jan 04, 2025)
6-35787889-C-T		not specified	Uncertain significance (Mar 07, 2024)
6-35787903-C-T		not specified	Uncertain significance (Dec 04, 2023)
6-35787933-G-C		not specified	Uncertain significance (Nov 06, 2023)
6-35787946-G-C		not specified	Uncertain significance (Mar 29, 2023)
6-35787960-C-T		not specified	Uncertain significance (Sep 12, 2023)
6-35787979-G-T		not specified	Uncertain significance (Apr 13, 2023)
6-35787982-A-C		not specified	Uncertain significance (Aug 11, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CLPSL1	protein_coding	protein_coding	ENST00000373861	3	12659

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0000217	0.167	124763	0	24	124787	0.0000962

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.185	70	65.8	1.06	0.00000392	763
Missense in Polyphen		14	12.376	1.1312		146
Synonymous	1.33	17	25.6	0.665	0.00000151	210
Loss of Function	-0.883	6	4.08	1.47	1.74e-7	43

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00123	0.00119
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	0.000133	0.000131
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Intolerance Scores

• rvis_EVS: 0.26
• rvis_percentile_EVS: 70.06

Haploinsufficiency Scores

• hipred: N
• hipred_score: 0.153

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

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