GNPDA1

protein-coding

glucosamine-6-phosphate deaminase 1

Gene summary

Glucosamine-6-phosphate deaminase (EC 3.5.99.6) is an allosteric enzyme that catalyzes the reversible conversion of D-glucosamine-6-phosphate into D-fructose-6-phosphate and ammonium (Arreola et al., 2003 [PubMed 12965206]).[supplied by OMIM, Jan 2010]

Previous symbols:

GNPI

MANE transcript

NM_005471.5

Inheritance

—

ClinVar variants

U:34

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.91

Max pathogenic AF

—

Genomic locus

chr5:141,991,749-142,013,041

External References & Databases

Ensembl (ENSG00000113552)

Transcript & Mutation Effects

hg38 • Region Span ~21.3 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 GNPDA1 variants in ClinVar

1 Conditions Cataloged

not specifiedTotal: 28

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_005471.5. 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						0
missense			30 clinvar			30
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			4 clinvar			4
Total	0	0	34	0	0	34

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 65 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_005471.5	RefSeq	NP_005462.1	6	MANE Select
ENST00000311337.11	Ensembl	ENSP00000311876.6	6	MANE Select
ENST00000500692.6	Ensembl	ENSP00000424275.1	6	Standard
ENST00000500692.7	Ensembl	ENSP00000424275.1	6	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

UDP-<i>N</i>-acetyl-D-galactosamine biosynthesis II
Amino sugar and nucleotide sugar metabolism - Homo sapiens (human)
Sialuria or French Type Sialuria
Sialuria or French Type Sialuria
Amino Sugar Metabolism

Biological Process

carbohydrate metabolic process
glucosamine catabolic process
N-acetylglucosamine catabolic process
UDP-N-acetylglucosamine biosynthetic process
generation of precursor metabolites and energy

Molecular Function

glucosamine-6-phosphate deaminase activity
protein binding
identical protein binding

Cellular Component

cytoplasm
cytosol
extracellular exosome

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000508177
Coding exons: 6
Length: 21293
Individuals with no LoFs: 125718
Homozygous LoFs: 0
Heterozygous LoFs: 30
Defined: 125748
p: 0.000119

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	1.79	104	169	0.614	0.00000916	1929
Missense (PolyPhen)		35	67.278	0.52023		776
Synonymous	-0.545	75	69.2	1.08	0.00000446	528
Loss of Function	0.284	11	12.1	0.912	5.74e-7	149

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00018	0.00018	rare
Latino/Admixed American	0.00018	0.00017	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0.000054	0.000054	rare
Finnish	0	0.0	absent
European (Non-Finnish)	0.00016	0.00016	rare
South Asian	0.000033	0.000033	rare
Other	0.00016	0.00016	rare

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: Seems to trigger calcium oscillations in mammalian eggs. These oscillations serve as the essential trigger for egg activation and early development of the embryo (By similarity). {ECO:0000250}.;

Recessive Scores

pRec: 0.164

Intolerance Scores

LoFtool: 0.637
RVIS EVS: -0.47
RVIS percentile EVS: 23.04

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: E
Indispensability score: 0.981

Gene Damage Prediction

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