GLUD2

glutamate dehydrogenase 2

Basic information

Region (hg38): X:121047609-121050094

Previous symbols: [ "GLUDP1" ]

Links

ENSG00000182890 ∙ NCBI:2747 ∙ OMIM:300144 ∙ HGNC:4336 ∙ Uniprot:P49448 ∙ 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 GLUD2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the GLUD2 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				3	1	4
missense			26	3	1	30
nonsense		1				1
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	1	26	6	2

Variants in GLUD2

This is a list of pathogenic ClinVar variants found in the GLUD2 region.

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

Position	Type	Phenotype	Significance	ClinVar
X-121047692-G-C		not specified	Uncertain significance (May 12, 2024)
X-121047722-G-T		not specified	Conflicting classifications of pathogenicity (Aug 28, 2023)
X-121047778-C-A			Benign (Apr 30, 2018)
X-121047800-C-T		not specified	Uncertain significance (Mar 28, 2024)
X-121047829-G-A		not specified	Uncertain significance (May 02, 2024)
X-121047829-G-T		not specified	Uncertain significance (Dec 17, 2023)
X-121047832-C-T		not specified	Uncertain significance (Jul 11, 2023)
X-121047856-G-T		not specified	Uncertain significance (Mar 17, 2023)
X-121047877-A-G		not specified	Uncertain significance (Feb 13, 2024)
X-121047940-G-A		Parkinson disease, late-onset	Uncertain significance (Mar 01, 2023)
X-121047941-T-G			Likely benign (Dec 01, 2022)
X-121047943-A-G		not specified	Uncertain significance (Apr 19, 2023)
X-121047979-C-T		not specified	Uncertain significance (Dec 09, 2023)
X-121048056-C-A			Likely benign (Jun 10, 2018)
X-121048057-G-T		not specified	Uncertain significance (Dec 22, 2023)
X-121048060-G-T		not specified	Uncertain significance (Dec 16, 2023)
X-121048096-C-T		Male infertility with azoospermia or oligozoospermia due to single gene mutation	Likely pathogenic (Sep 01, 2023)
X-121048135-C-T		not specified	Uncertain significance (Feb 16, 2023)
X-121048218-G-A			Likely benign (Mar 09, 2018)
X-121048223-G-T		not specified	Uncertain significance (Aug 12, 2022)
X-121048226-G-A		not specified	Uncertain significance (Aug 02, 2023)
X-121048238-G-C		not specified	Uncertain significance (May 27, 2022)
X-121048253-C-T		not specified	Uncertain significance (Apr 18, 2023)
X-121048361-T-C		not specified	Uncertain significance (Aug 16, 2021)
X-121048399-A-G		not specified	Uncertain significance (Jun 01, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
GLUD2	protein_coding	protein_coding	ENST00000328078	1	2333

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0315	0.826	0	0	0	0	0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.825	188	223	0.844	0.0000178	3665
Missense in Polyphen		40	66.994	0.59707		1149
Synonymous	-0.399	93	88.2	1.05	0.00000688	1150
Loss of Function	1.15	3	6.05	0.496	3.90e-7	145

LoF frequencies by population

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

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Important for recycling the chief excitatory neurotransmitter, glutamate, during neurotransmission.
• Pathway: Alanine, aspartate and glutamate metabolism - Homo sapiens (human);D-Glutamine and D-glutamate metabolism - Homo sapiens (human);Proximal tubule bicarbonate reclamation - Homo sapiens (human);Necroptosis - Homo sapiens (human);Nitrogen metabolism - Homo sapiens (human);Arginine biosynthesis - Homo sapiens (human);Glutamate Glutamine metabolism;Metabolism of amino acids and derivatives;Metabolism;ornithine <i>de novo </i> biosynthesis;Urea cycle and metabolism of arginine, proline, glutamate, aspartate and asparagine;Arginine Proline metabolism;glutamate biosynthesis/degradation;GABA shunt;Transcriptional activation of mitochondrial biogenesis;Mitochondrial biogenesis;Amino acid synthesis and interconversion (transamination);Organelle biogenesis and maintenance (Consensus)

Recessive Scores

• pRec: 0.620

Intolerance Scores

• loftool: 0.0904
• rvis_EVS: 0.15
• rvis_percentile_EVS: 64.51

Haploinsufficiency Scores

• pHI: 0.121
• hipred: N
• hipred_score: 0.187
• ghis: 0.559

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.961

Gene Damage Prediction

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

Gene ontology

• Biological process: glutamate metabolic process;glutamate biosynthetic process;glutamate catabolic process;oxidation-reduction process
• Cellular component: cytoplasm;mitochondrion
• Molecular function: glutamate dehydrogenase (NAD+) activity;glutamate dehydrogenase [NAD(P)+] activity;GTP binding;ADP binding;leucine binding