PRAF2

Chr X

PRA1 domain family member 2

Also known as: JM4, Yip6a

NCBI Gene: 11230ENSG00000243279UniProt: O60831OMIM: 300840

PRAF2 encodes a protein that facilitates L-glutamate transmembrane transport and is involved in ER/Golgi transport and vesicular trafficking at glutamatergic and GABAergic synapses. The gene shows moderate constraint against loss-of-function variants (pLI 0.74, LOEUF 0.67), suggesting intolerance to complete loss of protein function. Currently, no established disease associations have been reported for PRAF2 mutations in humans.

OMIMResearchSummary from RefSeq, UniProt
GOFmechanismLOEUF 0.67
Clinical Summary— PRAF2
⚡
Population Constraint (gnomAD)
Moderately constrained gene (pLI 0.74) — some intolerance to loss-of-function variants.
📋
ClinVar Variants
69 unique Pathogenic / Likely Pathogenic· 28 VUS of 100 total submissions
Explore recent and relevant literature in Research Assistant →

Population Genetics & Constraint

gnomAD v4 — loss-of-function & missense intolerance

gnomAD
Moderate LoF intolerance
LoF Constraint
0.67LOEUF
pLI 0.742
Z-score 1.96
OE 0.00 (0.00–0.67)
Moderately constrained

Typical tolerance to LoF variation

Missense Constraint
1.17Z-score
OE missense 0.63 (0.51–0.80)
52 obs / 81.9 exp
Tolerant

Mild missense constraint

Observed / Expected Ratios
LoF OE0.00 (0.00–0.67)
0≤0.351.4
Missense OE0.63 (0.51–0.80)
0≤0.61.4
Synonymous OE0.61
0≤1.21.6
LoF obs/exp: 0 / 4.5Missense obs/exp: 52 / 81.9Syn Z: 1.97
DN
0.5966th %ile
GOF
0.74top 25%
LOF
0.4234th %ile

The highest-scoring mechanism for this gene is gain-of-function.

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

100 submitted variants in ClinVar

ClinVar

Classification Summary

Pathogenic67
Likely Pathogenic2
VUS28
67
Pathogenic
2
Likely Pathogenic
28
VUS

Curated Variants Distribution

Classified variants from ClinVar · 5 ACMG categories

ClassificationLoFMissense + InframeNon-codingSynonymousTotal
Pathogenic
0
0
67
0
67
Likely Pathogenic
0
0
2
0
2
VUS
0
21
7
0
28
Likely Benign
0
0
0
0
0
Benign
0
0
0
0
0
Total02176097

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

View in ClinVar →

Protein Context — Lollipop Plot

PRAF2 · protein map & ClinVar variants

Showing all ClinVar variants across the protein. Search a specific variant to highlight its position.

3D Protein StructureAlphaFold

Clinical Trials

Active and recruiting trials from ClinicalTrials.gov

ClinicalTrials.gov

No active trials found for this gene.

Search ClinicalTrials.gov →
Clinical Literature
Open Research Assistant →
Full-Text Mentions
NLP-detected gene mentions in article bodies · via PubTator3
PubTator3
Top 4 full-text resultsSearch PubTator3 ↗
Key Publications
Landmark & review papers · by relevance
PubMed
Top 2 results · since 2015Search PubMed ↗
Recent Gene-Specific Literature
Gene in title · MEDLINE · newest first
Europe PMC
Top 5 resultsSearch Europe PMC ↗

External Resources

Links to major genomics databases and tools

Franklin by Genoox
AI-powered variant curation and clinical analysis
DECIPHER
Genomic variants and phenotypes in rare disease patients