PRAMEF15

Chr 1

PRAME family member 15

NCBI Gene: 653619 ENSG00000204501 UniProt: P0DUQ1

The protein functions as a ubiquitin-like ligase-substrate adaptor within the Cul2-RING ubiquitin ligase complex, facilitating proteasome-mediated protein degradation. The gene shows low constraint against loss-of-function variants (pLI 0.33, LOEUF 1.84), and no established Mendelian disease associations have been reported to date.

ResearchSummary from RefSeq

Enables ubiquitin-like ligase-substrate adaptor activity. Involved in proteasome-mediated ubiquitin-dependent protein catabolic process. Is active in Cul2-RING ubiquitin ligase complex. [provided by Alliance of Genome Resources, Jul 2025]

ResearchGenerating clinical summary…

MultiplemechanismLOEUF 1.84

Clinical Summary— PRAMEF15

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Population Constraint (gnomAD)

Constrained for loss-of-function variants (OE-LoF 0.00) despite low pLI — interpret in context.

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ClinVar Variants

3 VUS of 5 total submissions

Explore recent and relevant literature in Research Assistant →

Population Genetics & Constraint

gnomAD v4 — loss-of-function & missense intolerance

gnomAD

Tolerant — LoF & missense variants common in population

LoF Constraint?

1.84LOEUF

pLI 0.329

Z-score 0.62

OE 0.00 (0.00–1.84)

Tolerant

Highly tolerant — LoF variants common in population

Missense Constraint?

0.07Z-score

OE missense 0.89 (0.39–1.81)

3 obs / 3.4 exp

Tolerant

Mild missense constraint

Observed / Expected Ratios?

LoF OE?0.00 (0.00–1.84)

0≤0.351.4

Missense OE?0.89 (0.39–1.81)

0≤0.61.4

Synonymous OE?1.77

0≤1.21.6

LoF obs/exp: 0 / 0.4Missense obs/exp: 3 / 3.4Syn Z: -0.64

This gene — mechanism propensity

0.77top 25%

GOF

0.6345th %ile

LOF

0.1796th %ile

This gene has evidence for multiple mechanisms of pathogenicity (dominant-negative and gain-of-function). Both the Badonyi & Marsh prediction and the broader genomic evidence point to dominant-negative as the predominant mechanism. Different variants in this gene may act through different mechanisms — interpret in context of the specific variant.

DNprediction above median

GOFprediction above median

Note: In-silico variant effect predictors (SIFT, PolyPhen, REVEL, CADD) may underestimate pathogenicity of missense variants in genes with GOF or DN mechanisms. Consider functional evidence and clinical context.

Predictions from Badonyi M, Marsh JA. PLoS ONE. 2024;19(8):e0307312.

ClinVar Variant Classifications

5 submitted variants in ClinVar

ClinVar

Classification Summary

VUS3

Likely Benign2

VUS

Likely Benign

Curated Variants Distribution

Classified variants from ClinVar · 5 ACMG categories

Classification	Missense + Inframe	Synonymous	Total
Pathogenic	0	0	0
Likely Pathogenic	0	0	0
VUS	3	0	3
Likely Benign	1	1	2
Benign	0	0	0
Total	4	1	5

LoF = frameshift, stop gained/lost, canonical splice · Counts from ClinVar esearch · Updated hourly

View in ClinVar →

25 pathogenic / likely-pathogenic (of 32) ClinVar copy-number / structural variants overlap PRAMEF15 — these span large chromosomal regions, not the gene specifically, and are excluded from the counts above. Explore in CNV tools →