FCGRT p.Pro42=
c.126G>T · rs11551281 · VCV787141
Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
low-frequency (popmax 4.21%, eas)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | <0.2 | all four deltas below 0.2 · G>A here scores Δ0.53 · evaluated, not missing |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP -3.3 | GERP -2.9 |
| Overall | ||
| CADD | 4.465 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
4.21%
East Asian · 1,887/44,850 alleles
Filtering AF
4.05%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 3.99%
Overall
0.346%
5,578/1,613,280 alleles · low-frequency
exomes 3,796/1,461,138 · genomes 1,782/152,142 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 4.21% | 24 |
| African / African-American | 3.39% | 30 |
| South Asian | 0.713% | 140 |
| Remaining individualsnot grpmax-eligible | 0.424% | 236 |
| Admixed American | 0.252% | 397 |
| Middle Eastern | 0.0661% | 1,514 |
| Ashkenazi Jewishnot grpmax-eligible | 0.0135% | 7,390 |
| European (non-Finnish) | 0.00661% | 15,123 |
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
- FCGRT
- Protein
- p.Pro42=
- Coding
- c.126G>T
- MANE Select
- NM_001136019
- dbSNP
- rs11551281
- Type
- single nucleotide variant
- Location
- chr19:49513934 (GRCh38)
- Gene constraint
- LOEUF 0.706 · pLI 0.12 (gnomAD)
- Structure
- AlphaFold pLDDT 85.73 · 31 PDB
- Residue 42
- the 'alpha-1' region
Similar variants
- FCGRT p.Pro42Leu Uncertain significance ★ ⚠ same residue
- FCGRT p.Lys132Asn Benign ★★ same type
- FCGRT p.Thr340= Benign ★★ same type
- FCGRT p.Ala280Thr Uncertain significance ★ ⚠ same type
- FCGRT p.Ala280Val Uncertain significance ★ ⚠ same type
- FCGRT p.Ala283Thr Uncertain significance ★ ⚠ same type
- FCGRT p.Ala283Val Uncertain significance ★ ⚠ same type
- FCGRT p.Ala294Gly 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/fcgrt-p-pro42 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown