GART

phosphoribosylglycinamide formyltransferase, phosphoribosylglycinamide synthetase, phosphoribosylaminoimidazole synthetase, the group of Purinosome

Basic information

Region (hg38): 21:33503930-33543491

Previous symbols: [ "PRGS", "PGFT" ]

Links

ENSG00000159131 ∙ NCBI:2618 ∙ OMIM:138440 ∙ HGNC:4163 ∙ Uniprot:P22102 ∙ 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 GART gene.

• Inborn genetic diseases (36 variants)
• Intellectual disability (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the GART 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	2		36
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region		1				1
non coding						0
Total	0	0	34	2	0

Variants in GART

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

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

Position	Type	Phenotype	Significance	ClinVar
21-33504200-G-A		not specified	Uncertain significance (May 08, 2023)
21-33504418-A-C		not specified	Uncertain significance (Nov 14, 2023)
21-33504522-T-A		not specified	Uncertain significance (Sep 14, 2022)
21-33505621-T-C		not specified	Uncertain significance (Jan 19, 2024)
21-33506021-C-T		not specified	Uncertain significance (Apr 27, 2023)
21-33506044-T-C		not specified	Uncertain significance (Aug 22, 2023)
21-33506063-T-C		not specified	Uncertain significance (Dec 07, 2021)
21-33506081-C-G		not specified	Uncertain significance (Jan 10, 2022)
21-33506087-G-A		not specified	Uncertain significance (Dec 09, 2023)
21-33509785-G-A		not specified	Uncertain significance (Nov 07, 2022)
21-33509818-T-C		not specified	Uncertain significance (Mar 22, 2023)
21-33509842-G-A		not specified	Uncertain significance (Aug 17, 2022)
21-33509864-C-T		not specified	Uncertain significance (Jan 08, 2024)
21-33509867-A-G		not specified	Uncertain significance (Sep 08, 2023)
21-33509890-A-G		not specified	Uncertain significance (Jan 09, 2024)
21-33509912-G-A		not specified	Uncertain significance (Jul 25, 2023)
21-33517084-C-T		not specified	Uncertain significance (Nov 17, 2022)
21-33517133-G-A		not specified	Uncertain significance (Feb 15, 2023)
21-33517396-A-C		not specified	Uncertain significance (May 26, 2022)
21-33517404-A-C		Tracheoesophageal fistula	Likely pathogenic (Jul 01, 2019)
21-33517482-A-T		not specified	Uncertain significance (Feb 22, 2023)
21-33517572-G-T		not specified	Uncertain significance (Jun 29, 2023)
21-33517582-T-C		not specified	Uncertain significance (Feb 22, 2023)
21-33520402-A-G		not specified	Uncertain significance (Jan 07, 2022)
21-33520417-G-A		not specified	Uncertain significance (Sep 01, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
GART	protein_coding	protein_coding	ENST00000381831	21	39560

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.000277	1.00	125693	0	54	125747	0.000215

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.11	461	533	0.865	0.0000263	6532
Missense in Polyphen		142	202.23	0.70217		2494
Synonymous	0.0509	193	194	0.995	0.00000997	2060
Loss of Function	4.22	15	45.8	0.328	0.00000221	589

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000272	0.000271
Ashkenazi Jewish	0.00	0.00
East Asian	0.000221	0.000217
Finnish	0.000140	0.000139
European (Non-Finnish)	0.000332	0.000325
Middle Eastern	0.000221	0.000217
South Asian	0.000103	0.0000980
Other	0.000163	0.000163

dbNSFP

Source: dbNSFP

• Pathway: Antimetabolite Pathway - Folate Cycle, Pharmacodynamics;One carbon pool by folate - Homo sapiens (human);Purine metabolism - Homo sapiens (human);Methotrexate Pathway (Cancer Cell), Pharmacodynamics;Thiopurine Pathway, Pharmacokinetics/Pharmacodynamics;Purine Nucleoside Phosphorylase Deficiency;Mercaptopurine Action Pathway;Azathioprine Action Pathway;Xanthine Dehydrogenase Deficiency (Xanthinuria);Adenylosuccinate Lyase Deficiency;AICA-Ribosiduria;Thioguanine Action Pathway;Adenine phosphoribosyltransferase deficiency (APRT);Mitochondrial DNA depletion syndrome;Myoadenylate deaminase deficiency;Purine Metabolism;Molybdenum Cofactor Deficiency;Adenosine Deaminase Deficiency;Gout or Kelley-Seegmiller Syndrome;Lesch-Nyhan Syndrome (LNS);Xanthinuria type I;Xanthinuria type II;Folate Metabolism;One Carbon Metabolism;Metabolism of nucleotides;Folate metabolism;Metabolism;Nucleobase biosynthesis;Purine nucleotides nucleosides metabolism;tetrahydrofolate salvage from 5,10-methenyltetrahydrofolate;Purine ribonucleoside monophosphate biosynthesis;5-aminoimidazole ribonucleotide biosynthesis;purine nucleotides <i>de novo</i> biosynthesis (Consensus)

Recessive Scores

• pRec: 0.456

Intolerance Scores

• loftool: 0.823
• rvis_EVS: 0.74
• rvis_percentile_EVS: 86.34

Haploinsufficiency Scores

• pHI: 0.933
• hipred: N
• hipred_score: 0.463
• ghis: 0.544

Essentials

• essential_gene_CRISPR: E
• essential_gene_CRISPR2: E
• essential_gene_gene_trap: E
• gene_indispensability_pred: E
• gene_indispensability_score: 0.979

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Gart
• Phenotype: growth/size/body region phenotype; adipose tissue phenotype (the observable morphological and physiological characteristics of mammalian fat tissue that are manifested through development and lifespan); 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)

Zebrafish Information Network

• Gene name: gart
• Affected structure: iridophore
• Phenotype tag: abnormal
• Phenotype quality: decreased amount

Gene ontology

• Biological process: brainstem development;purine nucleotide biosynthetic process;'de novo' IMP biosynthetic process;glycine metabolic process;purine ribonucleoside monophosphate biosynthetic process;response to organic substance;response to inorganic substance;cerebellum development;cerebral cortex development;adenine biosynthetic process;tetrahydrofolate biosynthetic process
• Cellular component: cytosol;extracellular exosome
• Molecular function: phosphoribosylamine-glycine ligase activity;phosphoribosylformylglycinamidine cyclo-ligase activity;phosphoribosylglycinamide formyltransferase activity;ATP binding;metal ion binding