GDPGP1

GDP-D-glucose phosphorylase 1

Basic information

Region (hg38): 15:90233808-90245811

Previous symbols: [ "C15orf58" ]

Links

ENSG00000183208 ∙ NCBI:390637 ∙ OMIM:619240 ∙ HGNC:34360 ∙ Uniprot:Q6ZNW5 ∙ 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 GDPGP1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the GDPGP1 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			41	2		43
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	41	2	0

Variants in GDPGP1

This is a list of pathogenic ClinVar variants found in the GDPGP1 region.

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

Position	Type	Phenotype	Significance	ClinVar
15-90233828-C-G			Likely benign (Aug 04, 2023)
15-90233841-C-T			Likely benign (Dec 15, 2023)
15-90233847-C-A			Likely benign (Mar 04, 2022)
15-90233853-C-G			Uncertain significance (Aug 05, 2022)
15-90233866-C-A			Uncertain significance (Aug 21, 2022)
15-90233867-G-A		not specified	Uncertain significance (Feb 06, 2023)
15-90233873-C-T			Uncertain significance (Aug 22, 2021)
15-90233877-G-A			Likely benign (May 23, 2024)
15-90233877-GC-G			Pathogenic (Jun 24, 2024)
15-90233877-GCC-G		Epidermodysplasia verruciformis, susceptibility to, 3	Likely pathogenic (Feb 02, 2023)
15-90233878-C-T			Uncertain significance (Nov 25, 2020)
15-90233880-C-T			Likely benign (Oct 22, 2023)
15-90233885-TC-AA			Uncertain significance (Apr 08, 2022)
15-90234035-G-A		not specified	Benign (Jan 24, 2024)
15-90240916-T-G		not specified	Uncertain significance (Feb 21, 2024)
15-90240945-T-G		not specified	Uncertain significance (Oct 20, 2021)
15-90240961-A-G		not specified	Uncertain significance (Nov 09, 2023)
15-90240973-G-A		not specified	Likely benign (Feb 24, 2025)
15-90241026-G-A		not specified	Uncertain significance (Sep 01, 2021)
15-90241048-C-T		not specified	Uncertain significance (Jan 09, 2024)
15-90241137-C-T		not specified	Uncertain significance (Jun 22, 2021)
15-90241149-C-G		not specified	Likely benign (Oct 09, 2024)
15-90241150-G-T		not specified	Uncertain significance (Oct 04, 2024)
15-90241177-G-A		not specified	Uncertain significance (Dec 20, 2022)
15-90241191-G-A		not specified	Uncertain significance (Feb 07, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
GDPGP1	protein_coding	protein_coding	ENST00000558017	1	8276

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.19e-8	0.0560	125670	0	78	125748	0.000310

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.177	221	229	0.967	0.0000141	2458
Missense in Polyphen		87	93.841	0.9271		1022
Synonymous	-0.881	109	97.9	1.11	0.00000563	872
Loss of Function	-0.625	11	8.98	1.23	4.73e-7	94

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00226	0.00226
Ashkenazi Jewish	0.00	0.00
East Asian	0.000109	0.000109
Finnish	0.0000462	0.0000462
European (Non-Finnish)	0.000246	0.000246
Middle Eastern	0.000109	0.000109
South Asian	0.000163	0.000163
Other	0.000163	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Specific and highly efficient GDP-D-glucose phosphorylase regulating the levels of GDP-D-glucose in cells. {ECO:0000269|PubMed:21507950}.

Intolerance Scores

• rvis_EVS: 0.84
• rvis_percentile_EVS: 88.38

Haploinsufficiency Scores

• hipred: N
• hipred_score: 0.197
• ghis: 0.451

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Gdpgp1

Gene ontology

• Biological process: glucose metabolic process
• Cellular component: cytoplasm
• Molecular function: nucleotide binding;guanyl-nucleotide exchange factor activity;nucleotidyltransferase activity;hydrolase activity;GDP-D-glucose phosphorylase activity