GATD3

glutamine amidotransferase class 1 domain containing 3, the group of Glutamine amidotransferase class 1 domain containing

Basic information

Region (hg38): 21:44133609-44210114

Previous symbols: [ "C21orf33", "GATD3A" ]

Links

ENSG00000160221 ∙ NCBI:8209 ∙ OMIM:601659 ∙ HGNC:1273 ∙ Uniprot:P0DPI2 ∙ 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 GATD3 gene.

• not provided (3 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the GATD3 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						0
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding					1	1
Total	0	0	0	1	2

Variants in GATD3

This is a list of pathogenic ClinVar variants found in the GATD3 region.

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

Position	Type	Phenotype	Significance	ClinVar
21-44133714-T-T			Benign (Jun 06, 2017)
21-44133763-C-G			Likely benign (Apr 01, 2022)
21-44134139-T-G		not specified	Uncertain significance (Jul 14, 2021)
21-44137261-C-T			Benign (Jun 06, 2017)
21-44143322-C-G		not specified	Uncertain significance (Nov 12, 2021)
21-44143324-A-G		not specified	Uncertain significance (Jan 31, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
GATD3	protein_coding	protein_coding	ENST00000291577	7	12119

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0000297	0.570	125682	0	66	125748	0.000262

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.701	193	167	1.15	0.00000997	1702
Missense in Polyphen		81	71.118	1.139		695
Synonymous	0.853	69	78.6	0.878	0.00000561	563
Loss of Function	0.705	8	10.5	0.765	5.13e-7	121

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00131	0.00130
Ashkenazi Jewish	0.00	0.00
East Asian	0.000112	0.000109
Finnish	0.0000462	0.0000462
European (Non-Finnish)	0.000300	0.000290
Middle Eastern	0.000112	0.000109
South Asian	0.0000658	0.0000653
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Pathway: Gastric Cancer Network 1 (Consensus)

Recessive Scores

• pRec: 0.209

Intolerance Scores

• rvis_EVS: 0.22
• rvis_percentile_EVS: 68.27

Haploinsufficiency Scores

• pHI: 0.112
• hipred: N
• hipred_score: 0.294
• ghis: 0.466

Essentials

• essential_gene_gene_trap: N

Mouse Genome Informatics

• Gene name: D10Jhu81e

Zebrafish Information Network

• Gene name: es1
• Affected structure: retinal cone cell
• Phenotype tag: abnormal
• Phenotype quality: process quality

Gene ontology

• Cellular component: mitochondrion