PRTFDC1

protein-coding

phosphoribosyl transferase domain containing 1

Gene summary

Enables protein homodimerization activity. Predicted to be involved in purine ribonucleoside salvage. Predicted to be active in cytosol. [provided by Alliance of Genome Resources, Jul 2025]

MANE transcript

NM_020200.7

Inheritance

—

ClinVar variants

U:42B:2

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 1.15

Max pathogenic AF

—

Genomic locus

chr10:24,848,614-24,952,606

External References & Databases

Ensembl (ENSG00000099256)

Transcript & Mutation Effects

hg38 • Region Span ~104.0 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to PRTFDC1 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 39

not providedTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_020200.7. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous			1 clinvar		1 clinvar	2
missense			39 clinvar	1 clinvar		40
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			2 clinvar			2
Total	0	0	42	1	1	44

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 19 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_020200.7	RefSeq	NP_064585.1	9	MANE Select
ENST00000320152.11	Ensembl	ENSP00000318602.5	9	MANE Select
NM_001282786.2	RefSeq	NP_001269715.1	8	Standard
ENST00000376376.3	Ensembl	ENSP00000365556.3	4	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

purine ribonucleoside salvage
guanine salvage
GMP catabolic process

Molecular Function

nucleotide binding
magnesium ion binding
hypoxanthine phosphoribosyltransferase activity
protein binding
protein homodimerization activity

Cellular Component

cytoplasm

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000320152
Coding exons: 9
Length: 103998
Individuals with no LoFs: 125681
Homozygous LoFs: 0
Heterozygous LoFs: 64
Defined: 125745
p: 0.000255

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.437	115	129	0.892	0.00000660	1482
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00025	0.00025	rare
Latino/Admixed American	0.000058	0.000058	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0.00060	0.00060	rare
Finnish	0	0.0	absent
European (Non-Finnish)	0.00035	0.00035	rare
South Asian	0.00016	0.00016	rare
Other	0.00033	0.00033	rare

dbNSFP Gene Annotations

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

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: E
Indispensability score: 0.645

Gene Damage Prediction

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