GNPDA2

glucosamine-6-phosphate deaminase 2

Basic information

Region (hg38): 4:44682200-44726588

Links

ENSG00000163281 ∙ NCBI:132789 ∙ OMIM:613222 ∙ HGNC:21526 ∙ Uniprot:Q8TDQ7 ∙ 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 GNPDA2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the GNPDA2 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				1	1	2
missense			7			7
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	7	1	1

Variants in GNPDA2

This is a list of pathogenic ClinVar variants found in the GNPDA2 region.

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

Position	Type	Phenotype	Significance	ClinVar
4-44682328-T-C			Likely benign (Jun 27, 2022)
4-44682340-C-G		Developmental and epileptic encephalopathy, 40	Conflicting classifications of pathogenicity (Dec 25, 2023)
4-44682350-C-G			Uncertain significance (Feb 25, 2021)
4-44682352-G-A			Uncertain significance (May 23, 2023)
4-44682353-T-G			Uncertain significance (May 05, 2022)
4-44682359-ACTT-A			Uncertain significance (Oct 01, 2022)
4-44682372-C-T			Likely benign (Jul 13, 2022)
4-44682375-C-A		not specified	Uncertain significance (Jun 12, 2023)
4-44682375-C-T			Likely benign (Sep 01, 2022)
4-44682379-G-A		not specified	Uncertain significance (Nov 27, 2023)
4-44682384-G-A		GUF1-related disorder	Likely benign (May 08, 2023)
4-44682385-C-G			Uncertain significance (Feb 06, 2023)
4-44682389-C-T			Uncertain significance (Feb 12, 2022)
4-44682390-G-A			Uncertain significance (Aug 04, 2023)
4-44682414-A-G			Uncertain significance (Jan 14, 2022)
4-44682421-A-G			Benign (Feb 01, 2024)
4-44682438-C-T		Developmental and epileptic encephalopathy, 40	Benign (Aug 10, 2021)
4-44683207-T-TA		Developmental and epileptic encephalopathy, 40	Benign (Aug 10, 2021)
4-44683208-T-A		Developmental and epileptic encephalopathy, 40	Benign (Aug 10, 2021)
4-44683218-G-A			Likely benign (Dec 12, 2022)
4-44683219-AT-A			Benign (Feb 01, 2024)
4-44683219-A-AT			Benign (Jan 20, 2024)
4-44683226-T-C			Likely benign (Oct 13, 2023)
4-44683231-A-T		GUF1-related disorder	Likely benign (Aug 07, 2019)
4-44683236-T-G			Uncertain significance (Mar 08, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
GNPDA2	protein_coding	protein_coding	ENST00000295448	6	44396

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00848	0.939	125697	0	16	125713	0.0000636

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.09	106	143	0.743	0.00000673	1830
Missense in Polyphen		46	76.999	0.59741		1003
Synonymous	0.0642	48	48.6	0.988	0.00000249	491
Loss of Function	1.68	5	11.0	0.454	4.60e-7	168

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000660	0.0000660
Ashkenazi Jewish	0.000111	0.0000992
East Asian	0.00	0.00
Finnish	0.0000463	0.0000462
European (Non-Finnish)	0.0000999	0.0000967
Middle Eastern	0.00	0.00
South Asian	0.0000340	0.0000327
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Pathway: UDP-<i>N</i>-acetyl-D-galactosamine biosynthesis II;Amino sugar and nucleotide sugar metabolism - Homo sapiens (human);<i>N</i>-acetylglucosamine degradation II;Metabolism of carbohydrates;<i>N</i>-acetylglucosamine degradation I;Metabolism;Glycolysis;Glucose metabolism (Consensus)

Recessive Scores

• pRec: 0.140

Intolerance Scores

• rvis_EVS: -0.21
• rvis_percentile_EVS: 38.28

Haploinsufficiency Scores

• pHI: 0.356
• hipred: Y
• hipred_score: 0.579
• ghis: 0.650

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.901

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Gnpda2

Gene ontology

• Biological process: carbohydrate metabolic process;glucosamine catabolic process;N-acetylglucosamine catabolic process;UDP-N-acetylglucosamine biosynthetic process;N-acetylneuraminate catabolic process
• Cellular component: nucleus;cytoplasm;cytosol
• Molecular function: glucosamine-6-phosphate deaminase activity;protein binding;identical protein binding