GART
phosphoribosylglycinamide formyltransferase, phosphoribosylglycinamide synthetase, phosphoribosylaminoimidazole synthetase, the group of Purinosome
Basic information
Region (hg38): 21:33503931-33543491
Previous symbols: [ "PRGS", "PGFT" ]
Links
Phenotypes
GenCC
Source:
No genCC data.
ClinVar
This is a list of variants' phenotypes submitted to
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 | 39 | 41 | ||||
| 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 | 39 | 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) | ||
| 21-33509881-A-C | not specified | Uncertain significance (Apr 20, 2024) | ||
| 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) |
GnomAD
Source:
| 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:
- 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