SLC52A3 p.Phe3=
c.9C>T · rs139486822 · VCV262242
Benign/Likely benign
Multiple submitters
Classification
Benign/Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 10 submitters
gnomAD v4.1
Rare
low-frequency (popmax 1.21%, nfe)
Conditions
3
Inborn genetic diseases
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP 1.3 | GERP -0.32, phastCons 1 |
| Overall | ||
| CADD | 9.011 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
1.21%
European (non-Finnish) · 14,210/1,174,898 alleles
Filtering AF
1.19%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 1.19%
Overall
1%
16,045/1,600,526 alleles · low-frequency
exomes 14,939/1,460,714 · genomes 1,106/139,812 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| European (non-Finnish)grpmax | 1.21% | 83 |
| Admixed American | 1.02% | 98 |
| Remaining individualsnot grpmax-eligible | 0.861% | 116 |
| Finnishnot grpmax-eligible | 0.725% | 138 |
| Middle Eastern | 0.463% | 216 |
| African / African-American | 0.198% | 506 |
| Ashkenazi Jewishnot grpmax-eligible | 0.16% | 626 |
| South Asian | 0.0243% | 4,119 |
| East Asian | 0.0045% | 22,213 |
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
- SLC52A3
- Protein
- p.Phe3=
- Coding
- c.9C>T
- MANE Select
- NM_033409
- dbSNP
- rs139486822
- Type
- single nucleotide variant
- Location
- chr20:765766 (GRCh38)
- Gene constraint
- LOEUF 1.012 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
- Structure
- AlphaFold pLDDT 80.60 · 1 PDB
- Residue 3
- an α-helix
Similar variants
- SLC52A3 p.Phe3Leu Likely benign ★ same residue
- SLC52A3 p.Ala312Val Pathogenic/Likely pathogenic ★★ ⚠ same condition
- SLC52A3 p.Gln259Ter Pathogenic ★★ same condition
- SLC52A3 p.Glu184Ter Pathogenic ★★ same condition
- SLC52A3 p.Tyr213Ter Pathogenic ★★ same condition
- SLC52A3 p.Ala107Thr Uncertain significance ★★ ⚠ same condition
- SLC52A3 p.Ala107Val Uncertain significance ★★ ⚠ same condition
- SLC52A3 p.Ala216Thr Uncertain significance ★★ ⚠ same condition
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/slc52a3-p-phe3 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown