GLTPD2

glycolipid transfer protein domain containing 2

Basic information

Region (hg38): 17:4788964-4790589

Links

ENSG00000182327 ∙ NCBI:388323 ∙ ∙ HGNC:33756 ∙ Uniprot:A6NH11 ∙ 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 GLTPD2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the GLTPD2 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						0
missense			31	5		36
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	31	5	0

Variants in GLTPD2

This is a list of pathogenic ClinVar variants found in the GLTPD2 region.

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

Position	Type	Phenotype	Significance	ClinVar
17-4789028-G-A		not specified	Uncertain significance (Feb 14, 2023)
17-4789046-A-G		not specified	Likely benign (Sep 30, 2024)
17-4789084-C-G		not specified	Uncertain significance (Dec 21, 2022)
17-4789232-G-T		not specified	Likely benign (May 07, 2024)
17-4789235-C-T		not specified	Uncertain significance (Jun 17, 2024)
17-4789253-C-T		not specified	Uncertain significance (Mar 28, 2025)
17-4789259-C-T		not specified	Uncertain significance (Feb 28, 2025)
17-4789261-T-C		not specified	Uncertain significance (May 21, 2024)
17-4789271-G-A		not specified	Likely benign (Feb 19, 2025)
17-4789273-G-C		not specified	Uncertain significance (Feb 22, 2023)
17-4789277-C-A		not specified	Uncertain significance (Feb 22, 2025)
17-4789572-C-A		not specified	Uncertain significance (Apr 12, 2025)
17-4789575-G-A		not specified	Likely benign (May 02, 2024)
17-4789581-T-G		not specified	Uncertain significance (Feb 27, 2024)
17-4789582-G-A		not specified	Uncertain significance (Jan 02, 2024)
17-4789611-C-G		not specified	Uncertain significance (Oct 16, 2024)
17-4789613-A-T		not specified	Uncertain significance (Oct 01, 2024)
17-4789671-T-C		not specified	Uncertain significance (Sep 04, 2024)
17-4789788-C-T		not specified	Uncertain significance (Nov 29, 2023)
17-4789831-G-T		not specified	Uncertain significance (Nov 21, 2024)
17-4789848-C-G		not specified	Uncertain significance (Jan 01, 2025)
17-4789899-G-A		not specified	Uncertain significance (Jan 17, 2023)
17-4789926-C-T		not specified	Uncertain significance (Dec 11, 2024)
17-4789929-C-T		not specified	Uncertain significance (Jul 15, 2021)
17-4789939-C-A		not specified	Uncertain significance (Nov 15, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
GLTPD2	protein_coding	protein_coding	ENST00000331264	4	1432

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0000600	0.482	125615	0	29	125644	0.000115

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.156	143	138	1.04	0.00000678	1702
Missense in Polyphen		47	41.221	1.1402		604
Synonymous	0.113	65	66.2	0.982	0.00000337	659
Loss of Function	0.440	7	8.37	0.836	3.59e-7	96

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000265	0.000265
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000571	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.0000840	0.0000792
Middle Eastern	0.0000571	0.0000544
South Asian	0.000229	0.000229
Other	0.000506	0.000489

dbNSFP

Source: dbNSFP

Haploinsufficiency Scores

• pHI: 0.120
• hipred: N
• hipred_score: 0.204

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.0287

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Gltpd2

Gene ontology

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