GLTP

glycolipid transfer protein

Basic information

Region (hg38): 12:109850944-109880541

Links

ENSG00000139433 ∙ NCBI:51228 ∙ OMIM:608949 ∙ HGNC:24867 ∙ Uniprot:Q9NZD2 ∙ 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 GLTP gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the GLTP 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					2	2
missense			14			14
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	14	0	2

Variants in GLTP

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

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

Position	Type	Phenotype	Significance	ClinVar
12-109852596-T-C		not specified	Uncertain significance (Apr 23, 2024)
12-109852629-T-C		not specified	Uncertain significance (Jan 31, 2022)
12-109852643-C-T		not specified	Uncertain significance (Sep 16, 2021)
12-109855656-T-C		not specified	Uncertain significance (Mar 19, 2024)
12-109855685-G-A			Benign (May 11, 2017)
12-109855686-T-C		not specified	Uncertain significance (Feb 23, 2023)
12-109855692-C-T		not specified	Uncertain significance (Nov 07, 2022)
12-109855720-G-A		not specified	Uncertain significance (Apr 12, 2022)
12-109855729-C-T		not specified	Uncertain significance (Nov 03, 2023)
12-109855752-T-C		not specified	Uncertain significance (May 18, 2022)
12-109855756-T-C		not specified	Uncertain significance (Mar 06, 2023)
12-109855760-G-T			Benign (Nov 14, 2018)
12-109857580-T-C		not specified	Uncertain significance (Aug 10, 2021)
12-109857620-G-A		not specified	Uncertain significance (Jun 24, 2022)
12-109857644-A-G		not specified	Uncertain significance (Feb 17, 2023)
12-109858712-T-C		not specified	Uncertain significance (Dec 01, 2022)
12-109880306-G-C		not specified	Uncertain significance (May 09, 2024)
12-109880322-A-G		not specified	Uncertain significance (Aug 30, 2021)
12-109880370-G-A		not specified	Uncertain significance (Sep 29, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
GLTP	protein_coding	protein_coding	ENST00000318348	5	29546

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.115	0.861	125727	0	21	125748	0.0000835

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.525	110	127	0.869	0.00000749	1363
Missense in Polyphen		19	27.7	0.68592		392
Synonymous	1.28	45	57.3	0.785	0.00000390	401
Loss of Function	1.93	3	9.39	0.319	3.99e-7	112

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000163	0.000153
Ashkenazi Jewish	0.00	0.00
East Asian	0.000848	0.000816
Finnish	0.0000463	0.0000462
European (Non-Finnish)	0.0000176	0.0000176
Middle Eastern	0.000848	0.000816
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Accelerates the intermembrane transfer of various glycolipids. Catalyzes the transfer of various glycosphingolipids between membranes but does not catalyze the transfer of phospholipids. May be involved in the intracellular translocation of glucosylceramides. {ECO:0000269|PubMed:15329726, ECO:0000269|PubMed:15504043, ECO:0000269|PubMed:17980653, ECO:0000269|PubMed:18261224}.
• Pathway: Metabolism of lipids;Metabolism;Glycosphingolipid metabolism;Glycosphingolipid metabolism;Sphingolipid metabolism (Consensus)

Recessive Scores

• pRec: 0.156

Intolerance Scores

• loftool: 0.414
• rvis_EVS: -0.14
• rvis_percentile_EVS: 43.29

Haploinsufficiency Scores

• hipred: Y
• hipred_score: 0.507
• ghis: 0.569

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.227

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Gltp

Gene ontology

• Biological process: glycosphingolipid metabolic process;ceramide transport;glycolipid transport;intermembrane lipid transfer;ceramide 1-phosphate transport
• Cellular component: cytosol;membrane
• Molecular function: protein binding;lipid binding;glycolipid transporter activity;identical protein binding;glycolipid binding;intermembrane lipid transfer activity;ceramide 1-phosphate binding;ceramide 1-phosphate transporter activity