PRTFDC1

phosphoribosyl transferase domain containing 1

Basic information

Region (hg38): 10:24848613-24952606

Links

ENSG00000099256 ∙ NCBI:56952 ∙ OMIM:610751 ∙ HGNC:23333 ∙ Uniprot:Q9NRG1 ∙ 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 PRTFDC1 gene.

• Inborn genetic diseases (9 variants)
• not provided (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PRTFDC1 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
missense			8	1		9
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	8	1	1

Variants in PRTFDC1

This is a list of pathogenic ClinVar variants found in the PRTFDC1 region.

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

Position	Type	Phenotype	Significance	ClinVar
10-24849851-C-T		not specified	Uncertain significance (Nov 27, 2023)
10-24849854-T-C		not specified	Uncertain significance (Dec 27, 2023)
10-24851442-G-T		not specified	Uncertain significance (Jun 09, 2022)
10-24851444-T-C		not specified	Likely benign (Apr 18, 2023)
10-24855356-A-G		not specified	Uncertain significance (Nov 07, 2023)
10-24856937-T-C		not specified	Uncertain significance (Aug 09, 2021)
10-24856986-C-T		not specified	Uncertain significance (Aug 13, 2021)
10-24858397-C-A		not specified	Uncertain significance (Nov 08, 2022)
10-24872030-C-T		not specified	Uncertain significance (Aug 21, 2023)
10-24872046-A-G			Benign (Apr 20, 2018)
10-24937333-T-C		not specified	Uncertain significance (Aug 21, 2023)
10-24937362-T-C		not specified	Uncertain significance (Jul 08, 2022)
10-24942339-A-T		not specified	Uncertain significance (Aug 12, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PRTFDC1	protein_coding	protein_coding	ENST00000320152	9	103998

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
2.37e-13	0.00953	125681	0	64	125745	0.000255

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.437	115	129	0.892	0.00000660	1482
Missense in Polyphen		33	34.969	0.94369		489
Synonymous	0.0344	48	48.3	0.994	0.00000286	397
Loss of Function	-0.556	18	15.6	1.15	8.08e-7	186

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000304	0.000304
Ashkenazi Jewish	0.00	0.00
East Asian	0.000598	0.000598
Finnish	0.00	0.00
European (Non-Finnish)	0.000353	0.000352
Middle Eastern	0.000598	0.000598
South Asian	0.000163	0.000163
Other	0.000327	0.000326

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Has low, barely detectable phosphoribosyltransferase activity (in vitro). Binds GMP, IMP and alpha-D-5-phosphoribosyl 1-pyrophosphate (PRPP). Is not expected to contribute to purine metabolism or GMP salvage.

Recessive Scores

• pRec: 0.156

Intolerance Scores

• loftool: 0.441
• rvis_EVS: 0.08
• rvis_percentile_EVS: 60.09

Haploinsufficiency Scores

• pHI: 0.409
• hipred: N
• hipred_score: 0.219
• ghis: 0.531

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.645

Gene Damage Prediction

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

Gene ontology

• Biological process: purine ribonucleoside salvage;guanine salvage;GMP catabolic process
• Cellular component: cytoplasm
• Molecular function: nucleotide binding;magnesium ion binding;hypoxanthine phosphoribosyltransferase activity;protein binding;protein homodimerization activity