GATD1

glutamine amidotransferase class 1 domain containing 1, the group of Glutamine amidotransferase class 1 domain containing

Basic information

Region (hg38): 11:767220-777488

Previous symbols: [ "PDDC1" ]

Links

ENSG00000177225 ∙ NCBI:347862 ∙ ∙ HGNC:26616 ∙ Uniprot:Q8NB37 ∙ 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 GATD1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the GATD1 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			34	1		35
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	34	1	0

Variants in GATD1

This is a list of pathogenic ClinVar variants found in the GATD1 region.

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

Position	Type	Phenotype	Significance	ClinVar
11-771029-G-A		not specified	Uncertain significance (Aug 26, 2022)
11-771030-G-A		not specified	Uncertain significance (Sep 13, 2023)
11-771380-G-A		not specified	Uncertain significance (May 25, 2022)
11-771387-G-A		not specified	Uncertain significance (Apr 25, 2023)
11-771390-C-A		not specified	Uncertain significance (Mar 14, 2025)
11-771390-C-T		not specified	Uncertain significance (Feb 16, 2023)
11-771396-C-T		not specified	Uncertain significance (Jul 30, 2024)
11-771399-G-A		not specified	Uncertain significance (Dec 11, 2024)
11-771399-G-C		not specified	Uncertain significance (Dec 23, 2023)
11-771401-G-A		not specified	Uncertain significance (Jul 25, 2023)
11-771408-C-T		not specified	Likely benign (Jul 02, 2024)
11-772498-C-T		not specified	Uncertain significance (Jun 06, 2023)
11-772504-C-T		not specified	Uncertain significance (Nov 11, 2024)
11-773551-C-T		not specified	Uncertain significance (Jan 16, 2024)
11-773552-G-A		not specified	Uncertain significance (Jan 23, 2024)
11-773570-T-C		not specified	Uncertain significance (Nov 18, 2022)
11-773594-G-A		not specified	Uncertain significance (Sep 25, 2023)
11-773603-G-A		not specified	Uncertain significance (Aug 12, 2022)
11-773609-G-C		not specified	Uncertain significance (Aug 12, 2022)
11-773617-T-C		not specified	Uncertain significance (Jul 26, 2022)
11-774010-T-A		not specified	Uncertain significance (Mar 01, 2023)
11-774014-T-A		not specified	Uncertain significance (Dec 12, 2023)
11-774032-G-A		not specified	Uncertain significance (Nov 20, 2024)
11-774053-G-A		not specified	Uncertain significance (Jan 26, 2022)
11-774071-G-A		not specified	Uncertain significance (Nov 14, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
GATD1	protein_coding	protein_coding	ENST00000319863	8	10269

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.460	0.534	125616	0	50	125666	0.000199

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.389	125	138	0.907	0.00000935	1414
Missense in Polyphen		31	39.002	0.79484		337
Synonymous	-1.03	74	63.6	1.16	0.00000496	441
Loss of Function	2.34	2	9.97	0.201	4.24e-7	123

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000239	0.000239
Ashkenazi Jewish	0.00	0.00
East Asian	0.000435	0.000435
Finnish	0.00	0.00
European (Non-Finnish)	0.000299	0.000282
Middle Eastern	0.000435	0.000435
South Asian	0.000131	0.000131
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Intolerance Scores

• rvis_EVS: -0.6
• rvis_percentile_EVS: 17.91

Haploinsufficiency Scores

• pHI: 0.119
• hipred: N
• hipred_score: 0.378
• ghis: 0.615

Essentials

• essential_gene_gene_trap: N

Mouse Genome Informatics

• Gene name: Gatd1

Gene ontology

• Biological process: biological_process
• Cellular component: extracellular exosome
• Molecular function: molecular_function