CLPTM1L

CLPTM1 like

Basic information

Region (hg38): 5:1317751-1345099

Links

ENSG00000049656 ∙ NCBI:81037 ∙ OMIM:612585 ∙ HGNC:24308 ∙ Uniprot:Q96KA5 ∙ 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 CLPTM1L gene.

• Inborn genetic diseases (24 variants)
• not specified (2 variants)
• not provided (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CLPTM1L 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			26			26
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding					1	1
Total	0	0	26	0	1

Variants in CLPTM1L

This is a list of pathogenic ClinVar variants found in the CLPTM1L region.

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

Position	Type	Phenotype	Significance	ClinVar
5-1318375-C-T		CLPTM1L-related disorder	Likely benign (Dec 22, 2022)
5-1318389-G-A		not specified	Uncertain significance (Aug 12, 2021)
5-1318418-A-G		not specified	Uncertain significance (Jun 29, 2023)
5-1318433-C-T		not specified	Uncertain significance (Mar 07, 2023)
5-1318437-T-C		not specified	Uncertain significance (Jan 24, 2024)
5-1319565-C-A			Benign (Oct 28, 2020)
5-1320609-C-T		CLPTM1L-related disorder	Likely benign (Aug 10, 2019)
5-1320647-C-T		not specified	Uncertain significance (Sep 27, 2022)
5-1320652-T-A		not specified	Uncertain significance (Apr 22, 2022)
5-1322878-G-A		CLPTM1L-related disorder	Benign (May 09, 2019)
5-1322919-G-A		CLPTM1L-related disorder	Likely benign (Apr 24, 2019)
5-1323805-A-G		not specified	Uncertain significance (Mar 20, 2023)
5-1323830-C-T		not specified	Likely benign (Dec 16, 2023)
5-1323832-C-G		not specified	Uncertain significance (Oct 04, 2022)
5-1325759-C-T		CLPTM1L-related disorder	Benign (Aug 15, 2019)
5-1325771-C-T		not specified	Uncertain significance (Dec 20, 2022)
5-1325805-C-G		CLPTM1L-related disorder	Likely benign (Dec 26, 2019)
5-1330271-G-A		CLPTM1L-related disorder	Likely benign (Jun 08, 2019)
5-1330296-A-G		not specified	Uncertain significance (Nov 08, 2022)
5-1330333-C-T		not specified	Uncertain significance (Dec 15, 2022)
5-1330367-G-A		CLPTM1L-related disorder	Likely benign (Oct 15, 2020)
5-1330374-C-T		not specified	Uncertain significance (Feb 11, 2022)
5-1331803-C-A		not specified	Uncertain significance (Oct 10, 2023)
5-1331820-T-C		not specified	Uncertain significance (May 03, 2023)
5-1331869-G-C		not specified	Uncertain significance (Jan 31, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CLPTM1L	protein_coding	protein_coding	ENST00000320895	17	27356

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0000439	1.00	125709	0	38	125747	0.000151

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.567	301	330	0.912	0.0000201	3517
Missense in Polyphen		62	92.956	0.66698		1125
Synonymous	-1.52	174	150	1.16	0.0000109	1024
Loss of Function	3.12	13	32.0	0.406	0.00000145	363

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000579	0.0000579
Ashkenazi Jewish	0.00229	0.00209
East Asian	0.0000625	0.0000544
Finnish	0.0000462	0.0000462
European (Non-Finnish)	0.000108	0.0000967
Middle Eastern	0.0000625	0.0000544
South Asian	0.0000654	0.0000653
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Enhances cisplatin-mediated apoptosis, when overexpressed. {ECO:0000269|PubMed:11162647}.
• Pathway: Vitamin D Receptor Pathway (Consensus)

Recessive Scores

• pRec: 0.126

Intolerance Scores

• loftool: 0.421
• rvis_EVS: -0.6
• rvis_percentile_EVS: 18.19

Haploinsufficiency Scores

• pHI: 0.225
• hipred: Y
• hipred_score: 0.554
• ghis: 0.537

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.824

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Clptm1l

Gene ontology

• Biological process: apoptotic process
• Cellular component: membrane;integral component of membrane