CLPTM1

protein-coding

CLPTM1 regulator of GABA type A receptor forward trafficking

Gene summary

Predicted to enable GABA receptor binding activity. Predicted to be involved in regulation of T cell differentiation in thymus and regulation of postsynaptic membrane neurotransmitter receptor levels. Predicted to act upstream of or within inhibitory chemical synaptic transmission; memory; and regulation of synaptic plasticity. Located in membrane. [provided by Alliance of Genome Resources, Jun 2026]

MANE transcript

NM_001294.4

Inheritance

—

ClinVar variants

U:102B:29

Top phenotype

CLPTM1-related disorder

gnomAD constraint

pLI —, LoF o/e 0.17

Max pathogenic AF

—

Genomic locus

chr19:44,954,585-44,993,341

External References & Databases

Ensembl (ENSG00000104853)

Transcript & Mutation Effects

hg38 • Region Span ~38.8 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 CLPTM1 variants in ClinVar

3 Conditions Cataloged

not specifiedTotal: 83

CLPTM1-related disorderTotal: 38

not providedTotal: 11

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_001294.4. 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			1 clinvar	18 clinvar	7 clinvar	26
missense			93 clinvar	2 clinvar	2 clinvar	97
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			8 clinvar			8
Total	0	0	102	20	9	131

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 45 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_001294.4	RefSeq	NP_001285.1	14	MANE Select
ENST00000337392.10	Ensembl	ENSP00000336994.4	14	MANE Select
NM_001282175.2	RefSeq	NP_001269104.1	14	Standard
NM_001282176.2	RefSeq	NP_001269105.1	12	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

multicellular organism development
cell differentiation
regulation of T cell differentiation in thymus

Molecular Function

protein binding

Cellular Component

integral component of plasma membrane
external side of plasma membrane
membrane

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000337392
Coding exons: 14
Length: 38758
Individuals with no LoFs: 125738
Homozygous LoFs: 0
Heterozygous LoFs: 10
Defined: 125748
p: 0.0000398

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	2.93	259	430	0.602	0.0000292	4378
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0	0.0	absent
Latino/Admixed American	0.000058	0.000058	rare
Ashkenazi Jewish	0.000099	0.000099	rare
East Asian	0	0.0	absent
Finnish	0	0.0	absent
European (Non-Finnish)	0.000062	0.000062	rare
South Asian	0	0.0	absent
Other	0	0.0	absent

dbNSFP Gene Annotations

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

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: E
Indispensability score: 0.703

Gene Damage Prediction

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