GAD2

glutamate decarboxylase 2

Basic information

Region (hg38): 10:26216664-26304558

Links

ENSG00000136750 ∙ NCBI:2572 ∙ OMIM:138275 ∙ HGNC:4093 ∙ Uniprot:Q05329 ∙ 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 GAD2 gene.

• Inborn genetic diseases (19 variants)
• not provided (10 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the GAD2 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	3	4
missense			19	2	2	23
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding				1	1	2
Total	0	0	19	4	6

Variants in GAD2

This is a list of pathogenic ClinVar variants found in the GAD2 region.

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

Position	Type	Phenotype	Significance	ClinVar
10-26216879-G-C		not specified	Uncertain significance (May 24, 2023)
10-26217654-G-A		not specified	Uncertain significance (Oct 25, 2022)
10-26217862-G-A		not specified	Uncertain significance (Feb 16, 2023)
10-26217878-G-C		not specified	Uncertain significance (Dec 18, 2023)
10-26217883-G-A		not specified	Uncertain significance (Oct 26, 2022)
10-26217893-C-A		not specified	Uncertain significance (Dec 05, 2022)
10-26217930-C-T			Benign (May 18, 2018)
10-26217969-C-A		not specified	Uncertain significance (Nov 15, 2021)
10-26217983-A-C		not specified	Uncertain significance (Feb 15, 2023)
10-26219060-G-A		not specified	Uncertain significance (Jul 12, 2023)
10-26219128-A-C		not specified	Uncertain significance (Mar 01, 2024)
10-26219135-G-A		not specified	Uncertain significance (Oct 26, 2021)
10-26219214-C-A			Benign/Likely benign (Nov 01, 2022)
10-26219284-C-T			Likely benign (May 09, 2018)
10-26223932-T-C		not specified	Uncertain significance (Dec 20, 2023)
10-26223956-C-A		not specified	Uncertain significance (Sep 23, 2023)
10-26223976-A-G		not specified	Uncertain significance (Dec 21, 2022)
10-26224610-T-C			Benign (Dec 31, 2019)
10-26224622-G-A			Benign (Aug 22, 2018)
10-26224632-C-T			Benign (May 25, 2018)
10-26229726-G-A			Likely benign (Apr 10, 2018)
10-26229742-G-A			Likely benign (Jun 05, 2018)
10-26229751-A-T		not specified	Uncertain significance (Apr 07, 2022)
10-26245937-A-G		not specified	Uncertain significance (Jun 02, 2023)
10-26270630-G-A			Benign (Aug 18, 2018)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
GAD2	protein_coding	protein_coding	ENST00000376261	16	88252

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.751	0.249	125738	0	10	125748	0.0000398

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.53	258	337	0.766	0.0000175	3863
Missense in Polyphen		100	174.89	0.5718		2023
Synonymous	0.0258	123	123	0.997	0.00000688	1062
Loss of Function	4.42	7	35.4	0.198	0.00000167	409

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000906	0.0000906
Ashkenazi Jewish	0.0000992	0.0000992
East Asian	0.0000544	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.0000442	0.0000439
Middle Eastern	0.0000544	0.0000544
South Asian	0.0000329	0.0000327
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Catalyzes the production of GABA.
• Pathway: Alanine, aspartate and glutamate metabolism - Homo sapiens (human);Type I diabetes mellitus - Homo sapiens (human);GABAergic synapse - Homo sapiens (human);Butanoate metabolism - Homo sapiens (human);beta-Alanine metabolism - Homo sapiens (human);Taurine and hypotaurine metabolism - Homo sapiens (human);Alanine and aspartate metabolism;One carbon metabolism and related pathways;Biogenic Amine Synthesis;Alanine Aspartate Asparagine metabolism;Glutamate Glutamine metabolism;Methionine Cysteine metabolism;Neuronal System;glutamate dependent acid resistance;Methionine and cysteine metabolism;Urea cycle and metabolism of arginine, proline, glutamate, aspartate and asparagine;Arginine Proline metabolism;GABA shunt;GABA synthesis;GABA synthesis, release, reuptake and degradation;Neurotransmitter release cycle;Transmission across Chemical Synapses (Consensus)

Recessive Scores

• pRec: 0.862

Intolerance Scores

• loftool: 0.533
• rvis_EVS: -0.11
• rvis_percentile_EVS: 45.36

Haploinsufficiency Scores

• pHI: 0.461
• hipred: Y
• hipred_score: 0.850
• ghis: 0.582

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.995

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Gad2
• Phenotype: craniofacial phenotype; muscle phenotype; homeostasis/metabolism phenotype; endocrine/exocrine gland phenotype; reproductive system 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); normal phenotype; growth/size/body region 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); digestive/alimentary phenotype; immune system phenotype; respiratory system phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan)

Gene ontology

• Biological process: glutamate decarboxylation to succinate;chemical synaptic transmission;neurotransmitter biosynthetic process;response to drug
• Cellular component: Golgi membrane;cytosol;plasma membrane;cell junction;axon;synaptic vesicle membrane;anchored component of membrane;presynaptic membrane;perinuclear region of cytoplasm;inhibitory synapse;clathrin-sculpted gamma-aminobutyric acid transport vesicle membrane
• Molecular function: glutamate decarboxylase activity;protein binding;glutamate binding;pyridoxal phosphate binding;protein heterodimerization activity