ADPGK

ADP dependent glucokinase

Basic information

Region (hg38): 15:72751294-72785846

Links

ENSG00000159322 ∙ NCBI:83440 ∙ OMIM:611861 ∙ HGNC:25250 ∙ Uniprot:Q9BRR6 ∙ 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 ADPGK gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ADPGK 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			30			30
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	30	0	0

Variants in ADPGK

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

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

Position	Type	Phenotype	Significance	ClinVar
15-72752413-A-C		not specified	Uncertain significance (Jan 23, 2023)
15-72752549-G-A		not specified	Uncertain significance (Feb 06, 2024)
15-72752564-C-T		not specified	Uncertain significance (Jun 11, 2021)
15-72752570-G-T		not specified	Uncertain significance (Feb 16, 2023)
15-72752576-A-G		not specified	Uncertain significance (Sep 22, 2023)
15-72752692-G-T		not specified	Uncertain significance (Dec 28, 2023)
15-72752882-G-A		not specified	Uncertain significance (Jul 09, 2021)
15-72755566-A-G		not specified	Uncertain significance (Apr 25, 2023)
15-72755567-T-C		not specified	Uncertain significance (Apr 09, 2024)
15-72755636-C-G		not specified	Uncertain significance (Nov 28, 2023)
15-72756309-G-C		not specified	Uncertain significance (Sep 30, 2021)
15-72756319-C-G		not specified	Uncertain significance (May 14, 2024)
15-72756358-C-T		not specified	Uncertain significance (Sep 14, 2021)
15-72756391-C-T		not specified	Uncertain significance (Jan 23, 2024)
15-72756408-C-T		not specified	Uncertain significance (Dec 30, 2023)
15-72756421-G-A		not specified	Uncertain significance (Apr 01, 2024)
15-72760425-T-C		not specified	Uncertain significance (Dec 16, 2023)
15-72760428-G-A		not specified	Uncertain significance (Apr 26, 2023)
15-72760492-A-C		not specified	Uncertain significance (Sep 28, 2022)
15-72760500-T-C		not specified	Uncertain significance (Dec 19, 2022)
15-72771811-T-C		not specified	Uncertain significance (Jan 23, 2023)
15-72771841-T-C		not specified	Uncertain significance (Dec 22, 2023)
15-72774894-G-A		not specified	Uncertain significance (Mar 15, 2024)
15-72774898-C-G		not specified	Uncertain significance (Sep 21, 2023)
15-72774909-T-A		not specified	Uncertain significance (Mar 29, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ADPGK	protein_coding	protein_coding	ENST00000311669	7	34478

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00522	0.990	124769	0	26	124795	0.000104

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.02	211	257	0.822	0.0000127	3183
Missense in Polyphen		49	71.659	0.6838		846
Synonymous	-0.0178	106	106	1.00	0.00000592	1036
Loss of Function	2.46	7	18.4	0.381	9.54e-7	211

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000339	0.000274
Ashkenazi Jewish	0.00	0.00
East Asian	0.000167	0.000167
Finnish	0.00	0.00
European (Non-Finnish)	0.000106	0.000106
Middle Eastern	0.000167	0.000167
South Asian	0.000131	0.000131
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Catalyzes the phosphorylation of D-glucose to D-glucose 6-phosphate using ADP as the phosphate donor. GDP and CDP can replace ADP, but with reduced efficiency (By similarity). {ECO:0000250}.
• Pathway: Glycolysis / Gluconeogenesis - Homo sapiens (human);miR-targeted genes in epithelium - TarBase;miR-targeted genes in leukocytes - TarBase;miR-targeted genes in lymphocytes - TarBase;Metabolism of carbohydrates;Metabolism;Glycolysis;Glucose metabolism (Consensus)

Recessive Scores

• pRec: 0.147

Intolerance Scores

• loftool: 0.488
• rvis_EVS: 0.13
• rvis_percentile_EVS: 63.2

Haploinsufficiency Scores

• pHI: 0.353
• hipred: N
• hipred_score: 0.331
• ghis: 0.543

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.492

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Adpgk
• Phenotype: hematopoietic system phenotype; immune system phenotype; growth/size/body region phenotype; adipose tissue phenotype (the observable morphological and physiological characteristics of mammalian fat tissue that are manifested through development and lifespan); homeostasis/metabolism phenotype

Gene ontology

• Biological process: glucose metabolic process;canonical glycolysis
• Cellular component: extracellular region;endoplasmic reticulum;endoplasmic reticulum membrane;membrane
• Molecular function: ADP-specific glucokinase activity;metal ion binding