GNPDA1

glucosamine-6-phosphate deaminase 1

Basic information

Region (hg38): 5:141991749-142013041

Previous symbols: [ "GNPI" ]

Links

ENSG00000113552

∙ NCBI:10007 ∙ OMIM:601798 ∙ HGNC:4417 ∙ Uniprot:P46926 ∙ 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 GNPDA1 gene.

not_specified (25 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the GNPDA1 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000005471.5. Only rare variants are included in the table.

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.

Effect	PathogenicP	Likely pathogenicLP	VUSVUS	Likely benignLB	BenignB	Sum
synonymous						0
missense			25 clinvar			25
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	25	0	0

Loading clinvar variants...

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
GNPDA1	protein_coding	protein_coding	ENST00000508177	6	21293

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.60e-7	0.237	125718	0	30	125748	0.000119

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.79	104	169	0.614	0.00000916	1929
Missense in 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

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000360	0.000360
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000544	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.000160	0.000158
Middle Eastern	0.0000544	0.0000544
South Asian	0.0000327	0.0000327
Other	0.000164	0.000163

dbNSFP

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}.;
Pathway: UDP-N-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;G(M2)-Gangliosidosis: Variant B, Tay-sachs disease;Tay-Sachs Disease;Salla Disease/Infantile Sialic Acid Storage Disease;N-acetylglucosamine degradation II;Aminosugars metabolism;Metabolism of carbohydrates;Fructose Mannose metabolism;N-acetylglucosamine degradation I;Metabolism;Glycolysis;Glucose metabolism (Consensus)

Recessive Scores

pRec: 0.164

Intolerance Scores

loftool: 0.637
rvis_EVS: -0.47
rvis_percentile_EVS: 23.04

Haploinsufficiency Scores

pHI: 0.255
hipred: Y
hipred_score: 0.528
ghis: 0.587

Essentials

essential_gene_CRISPR: N
essential_gene_CRISPR2: N
essential_gene_gene_trap: N
gene_indispensability_pred: E
gene_indispensability_score: 0.981

Gene Damage Prediction

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

Mouse Genome Informatics

Gene name: Gnpda1
Phenotype: mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); embryo phenotype; renal/urinary system phenotype; nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan); growth/size/body region phenotype;

Gene ontology

Biological process: carbohydrate metabolic process;glucosamine catabolic process;N-acetylglucosamine catabolic process;UDP-N-acetylglucosamine biosynthetic process;generation of precursor metabolites and energy;single fertilization;N-acetylneuraminate catabolic process
Cellular component: cytoplasm;cytosol;extracellular exosome
Molecular function: glucosamine-6-phosphate deaminase activity;protein binding;identical protein binding