CLPTM1L

CLPTM1 like

Basic information

Region (hg38): 5:1317752-1345099

Links

ENSG00000049656NCBI:81037OMIM:612585HGNC:24308Uniprot:Q96KA5AlphaFoldGenCCjaxSfariGnomADPubmedClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the CLPTM1L gene.

  • not_specified (77 variants)
  • CLPTM1L-related_disorder (19 variants)
  • Prostate_cancer (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. These statistics are base on transcript: NM_000030782.5. Only rare variants are included in the table.

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.

EffectPLPVUSLBBSum
synonymous
8
clinvar
5
clinvar
13
missense
74
clinvar
4
clinvar
2
clinvar
80
nonsense
0
start loss
0
frameshift
0
splice donor/acceptor (+/-2bp)
0
Total 0 0 74 12 7
Loading clinvar variants...

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
CLPTM1Lprotein_codingprotein_codingENST00000320895 1727356
pLI Probability
LOF Intolerant
pRec Probability
LOF Recessive
Individuals with
no LOFs
Individuals with
Homozygous LOFs
Individuals with
Heterozygous LOFs
Defined p
0.00004391.001257090381257470.000151
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense0.5673013300.9120.00002013517
Missense in Polyphen6292.9560.666981125
Synonymous-1.521741501.160.00001091024
Loss of Function3.121332.00.4060.00000145363

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.00005790.0000579
Ashkenazi Jewish0.002290.00209
East Asian0.00006250.0000544
Finnish0.00004620.0000462
European (Non-Finnish)0.0001080.0000967
Middle Eastern0.00006250.0000544
South Asian0.00006540.0000653
Other0.000.00

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

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium

Mouse Genome Informatics

Gene name
Clptm1l
Phenotype

Gene ontology

Biological process
apoptotic process
Cellular component
membrane;integral component of membrane
Molecular function