CLPTM1

CLPTM1 regulator of GABA type A receptor forward trafficking

Basic information

Region (hg38): 19:44954584-44993341

Links

ENSG00000104853 ∙ NCBI:1209 ∙ OMIM:604783 ∙ HGNC:2087 ∙ Uniprot:O96005 ∙ 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 CLPTM1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CLPTM1 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				17	7	24
missense			41	1	2	44
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region				3	1	4
non coding				1	1	2
Total	0	0	41	19	10

Variants in CLPTM1

This is a list of pathogenic ClinVar variants found in the CLPTM1 region.

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

Position	Type	Phenotype	Significance	ClinVar
19-44955086-G-T		CLPTM1-related disorder	Likely benign (May 28, 2019)
19-44955400-C-T		not specified	Uncertain significance (May 14, 2024)
19-44955401-G-A		CLPTM1-related disorder	Likely benign (Apr 24, 2023)
19-44955416-G-A			Likely benign (Jun 01, 2018)
19-44955435-G-A		not specified	Uncertain significance (May 12, 2024)
19-44955448-G-C		not specified	Uncertain significance (Oct 29, 2021)
19-44955454-G-A		CLPTM1-related disorder • not specified	Uncertain significance (Jan 09, 2024)
19-44955463-G-A		not specified	Uncertain significance (Nov 16, 2021)
19-44961958-C-A		CLPTM1-related disorder	Likely benign (Jul 01, 2021)
19-44961984-G-A		not specified	Uncertain significance (Feb 23, 2023)
19-44961994-C-T		not specified	Uncertain significance (May 30, 2024)
19-44962000-C-T		not specified	Uncertain significance (Nov 30, 2022)
19-44962025-G-A		CLPTM1-related disorder	Benign (Apr 30, 2019)
19-44973099-C-T		CLPTM1-related disorder	Likely benign (Aug 04, 2021)
19-44973121-C-T		not specified	Uncertain significance (Apr 19, 2024)
19-44973122-G-A		not specified	Uncertain significance (Jan 10, 2023)
19-44973150-G-A		CLPTM1-related disorder	Likely benign (Apr 09, 2019)
19-44973156-C-T		CLPTM1-related disorder	Benign (Apr 11, 2019)
19-44973157-G-A		not specified	Uncertain significance (Mar 25, 2024)
19-44973165-T-C			Benign (Jun 15, 2020)
19-44973171-C-T		CLPTM1-related disorder	Likely benign (Mar 22, 2019)
19-44974474-T-C		CLPTM1-related disorder	Benign (Apr 03, 2019)
19-44974485-A-G		not specified	Uncertain significance (Oct 31, 2022)
19-44974487-G-A		not specified	Uncertain significance (Nov 07, 2022)
19-44974529-G-A		not specified	Uncertain significance (Mar 19, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CLPTM1	protein_coding	protein_coding	ENST00000337392	14	38758

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.958	0.0423	125738	0	10	125748	0.0000398

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.93	259	430	0.602	0.0000292	4378
Missense in Polyphen		59	145.52	0.40545		1580
Synonymous	0.284	183	188	0.974	0.0000147	1310
Loss of Function	4.66	6	36.3	0.165	0.00000192	370

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000580	0.0000580
Ashkenazi Jewish	0.0000994	0.0000992
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000618	0.0000615
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May play a role in T-cell development. {ECO:0000250}.

Recessive Scores

• pRec: 0.122

Intolerance Scores

• loftool: 0.0752
• rvis_EVS: -1.15
• rvis_percentile_EVS: 6.27

Haploinsufficiency Scores

• pHI: 0.596
• hipred: Y
• hipred_score: 0.662
• ghis: 0.605

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.703

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Clptm1

Gene ontology

• Biological process: multicellular organism development;cell differentiation;regulation of T cell differentiation in thymus
• Cellular component: integral component of plasma membrane;external side of plasma membrane;membrane
• Molecular function: protein binding