CLPTM1L

protein-coding

CLPTM1 like

Gene summary

The protein encoded by this gene is a membrane protein whose overexpression in cisplatin-sensitive cells causes apoptosis. Polymorphisms in this gene have been reported to increase susceptibility to several cancers, including lung, pancreatic, and breast cancers. [provided by RefSeq, Nov 2015]

MANE transcript

NM_030782.5

Inheritance

—

ClinVar variants

U:98B:20

Top phenotype

CLPTM1L-related disorder

gnomAD constraint

pLI —, LoF o/e 0.41

Max pathogenic AF

—

Genomic locus

chr5:1,317,752-1,345,099

External References & Databases

Ensembl (ENSG00000049656)

Transcript & Mutation Effects

hg38 • Region Span ~27.3 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to CLPTM1L variants in ClinVar

4 Conditions Cataloged

not specifiedTotal: 86

CLPTM1L-related disorderTotal: 20

not providedTotal: 1

Prostate cancerTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_030782.5. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous				8 clinvar	5 clinvar	13
missense			88 clinvar	5 clinvar	2 clinvar	95
nonsense						0
start loss						0
frameshift			1 clinvar			1
splice donor/acceptor (+/-2bp)			9 clinvar			9
Total	0	0	98	13	7	118

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 57 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_030782.5	RefSeq	NP_110409.2	17	MANE Select
ENST00000320895.10	Ensembl	ENSP00000313854.5	17	MANE Select
ENST00000507807.3	Ensembl	ENSP00000423321.1	14	Standard
ENST00000507807.4	Ensembl	ENSP00000423321.1	14	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

Vitamin D Receptor Pathway

Biological Process

apoptotic process

Cellular Component

membrane
integral component of membrane

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000320895
Coding exons: 17
Length: 27356
Individuals with no LoFs: 125709
Homozygous LoFs: 0
Heterozygous LoFs: 38
Defined: 125747
p: 0.000151

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.567	301	330	0.912	0.0000201	3517
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0	0.0	absent
Latino/Admixed American	0.000058	0.000058	rare
Ashkenazi Jewish	0.0023	0.0021	notable
East Asian	0.000062	0.000054	rare
Finnish	0.000046	0.000046	rare
European (Non-Finnish)	0.00011	0.000097	rare
South Asian	0.000065	0.000065	rare
Other	0	0.0	absent

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: Enhances cisplatin-mediated apoptosis, when overexpressed. {ECO:0000269|PubMed:11162647}.;

Recessive Scores

pRec: 0.126

Intolerance Scores

LoFtool: 0.421
RVIS EVS: -0.6
RVIS percentile EVS: 18.19

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: E
Indispensability score: 0.824

Gene Damage Prediction

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