GADL1

glutamate decarboxylase like 1

Basic information

Region (hg38): 3:30726197-30894661

Links

ENSG00000144644 ∙ NCBI:339896 ∙ OMIM:615601 ∙ HGNC:27949 ∙ Uniprot:Q6ZQY3 ∙ 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 GADL1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the GADL1 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						0
missense			36	1		37
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	36	1	0

Variants in GADL1

This is a list of pathogenic ClinVar variants found in the GADL1 region.

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

Position	Type	Phenotype	Significance	ClinVar
3-30728297-C-T		not specified	Uncertain significance (May 23, 2024)
3-30728298-G-A		not specified	Uncertain significance (Feb 06, 2024)
3-30728322-C-G		not specified	Uncertain significance (May 04, 2023)
3-30728336-T-C		not specified	Uncertain significance (Jan 31, 2024)
3-30728348-C-T		not specified	Uncertain significance (Jul 13, 2021)
3-30728370-T-A		not specified	Uncertain significance (Sep 26, 2022)
3-30728408-G-A		not specified	Uncertain significance (Jan 23, 2023)
3-30778217-T-C		not specified	Uncertain significance (Nov 07, 2022)
3-30786358-C-T		not specified	Uncertain significance (Oct 26, 2021)
3-30800946-T-C		not specified	Uncertain significance (Mar 02, 2023)
3-30800950-A-C		not specified	Uncertain significance (Feb 28, 2023)
3-30800968-A-G		not specified	Uncertain significance (Apr 13, 2022)
3-30801002-G-C		not specified	Uncertain significance (Feb 09, 2022)
3-30801066-G-C		not specified	Likely benign (Jul 06, 2021)
3-30833916-C-G		not specified	Uncertain significance (Jun 22, 2021)
3-30834253-G-A		not specified	Uncertain significance (Apr 17, 2023)
3-30834255-C-T		not specified	Uncertain significance (Dec 01, 2022)
3-30839008-G-A		not specified	Uncertain significance (Aug 30, 2022)
3-30839014-G-A		not specified	Uncertain significance (May 20, 2024)
3-30839049-A-G		not specified	Uncertain significance (Sep 12, 2023)
3-30839095-C-A		not specified	Uncertain significance (Sep 13, 2023)
3-30839096-A-C		EBV-positive nodal T- and NK-cell lymphoma	Likely benign (-)
3-30839103-G-A		not specified	Uncertain significance (Aug 04, 2023)
3-30844232-T-C		not specified	Uncertain significance (Sep 26, 2023)
3-30844393-T-A		not specified	Uncertain significance (Jan 23, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
GADL1	protein_coding	protein_coding	ENST00000282538	15	168566

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.37e-21	0.000674	125212	3	531	125746	0.00213

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.724	306	272	1.12	0.0000133	3443
Missense in Polyphen		129	108.72	1.1865		1378
Synonymous	-1.08	110	96.5	1.14	0.00000498	924
Loss of Function	-0.287	31	29.3	1.06	0.00000131	385

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000377	0.000376
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000547	0.0000544
Finnish	0.0000462	0.0000462
European (Non-Finnish)	0.000248	0.000211
Middle Eastern	0.0000547	0.0000544
South Asian	0.0164	0.0162
Other	0.00148	0.00147

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May catalyze the decarboxylation of L-aspartate, 3- sulfino-L-alanine (cysteine sulfinic acid), and L-cysteate to beta-alanine, hypotaurine and taurine, respectively. Does not exhibit any decarboxylation activity toward glutamate. {ECO:0000269|PubMed:23038267}.
• Pathway: beta-Alanine metabolism - Homo sapiens (human);Pantothenate and CoA biosynthesis - Homo sapiens (human);Taurine and hypotaurine metabolism - Homo sapiens (human);Metabolism of amino acids and derivatives;Metabolism;Amino acid synthesis and interconversion (transamination) (Consensus)

Recessive Scores

• pRec: 0.123

Intolerance Scores

• loftool: 0.926
• rvis_EVS: 0.55
• rvis_percentile_EVS: 81.6

Haploinsufficiency Scores

• pHI: 0.144
• hipred: N
• hipred_score: 0.251

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.252

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Gadl1

Gene ontology

• Biological process: sulfur amino acid catabolic process;cellular amino acid biosynthetic process
• Cellular component: cytosol
• Molecular function: aspartate 1-decarboxylase activity;sulfinoalanine decarboxylase activity;carboxy-lyase activity;pyridoxal phosphate binding