GPR39 p.Ser147=
c.441G>A · rs140240801 · VCV711116
Benign
Single submitter
Classification
Benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
rare (popmax 0.629%, afr)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | <0.2 | no splice effect predicted · four deltas, not one · how we know |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP -10 | GERP -3.4 |
| Overall | ||
| CADD | 0.502 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.629%
African / African-American · 472/75,032 alleles
Filtering AF
0.582%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.564%
Overall
0.035%
565/1,614,102 alleles · rare
exomes 295/1,461,874 · genomes 270/152,228 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.629% | 159 |
| Ashkenazi Jewishnot grpmax-eligible | 0.0777% | 1,287 |
| Admixed American | 0.0517% | 1,936 |
| Remaining individualsnot grpmax-eligible | 0.0464% | 2,156 |
| Middle Eastern | 0.033% | 3,030 |
| South Asian | 0.0022% | 45,535 |
| European (non-Finnish) | 0.000508% | 196,669 |
Rarity supports pathogenicity (ACMG PM2); frequency above a disease-specific BA1/BS1 threshold argues against it. A variant frequent in one ancestry group can be near-absent in others, so a single global figure can mislead.
Variant & gene context
- Gene
- GPR39
- Protein
- p.Ser147=
- Coding
- c.441G>A
- MANE Select
- NM_001508
- dbSNP
- rs140240801
- Type
- single nucleotide variant
- Location
- chr2:132417483 (GRCh38)
- Gene constraint
- LOEUF 1.645 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 76.53
Similar variants
- GPR39 p.Ser147Leu Uncertain significance ★ ⚠ same residue
- GPR39 p.Asn212Ser Benign ★★ same type
- GPR39 p.Ala277Gly Uncertain significance ★ ⚠ same type
- GPR39 p.Ala437Ser Uncertain significance ★ ⚠ same type
- GPR39 p.Arg278Thr Uncertain significance ★ ⚠ same type
- GPR39 p.Arg386Gly Uncertain significance ★ ⚠ same type
- GPR39 p.Asn434Ser Uncertain significance ★ ⚠ same type
- GPR39 p.Asp10His Uncertain significance ★ ⚠ same type
Built on 18 open, versioned datasets — ClinVar, gnomAD, AlphaMissense, REVEL, ClinGen & more — plus Sugi Variant's own cross-source analysis. Source data 2026-01–2026-10, ClinVar 2026-10. Full sources & versions →
Cite Sugi Variant
Gür T. Sugi Variant: A Deterministic Per-Variant Germline Reference from a Knowledge Graph for Humans and AI Agents. 2026. doi:10.5281/zenodo.21509445. This variant: https://sugi.bio/variant/gpr39-p-ser147 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown