FIGLA p.Arg48=
c.142C>A · VCV4822112
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0216%, amr)
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 4.9 | GERP 0.89, phastCons 1 |
| Overall | ||
| CADD | 13.68 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0216%
Admixed American · 11/50,906 alleles
Filtering AF
0.012%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00933%
Overall
0.0011%
17/1,542,988 alleles · ultra-rare
exomes 14/1,390,742 · genomes 3/152,246 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Admixed Americangrpmax | 0.0216% | 4,628 |
| Remaining individualsnot grpmax-eligible | 0.005% | 19,997 |
| European (non-Finnish) | 0.000262% | 382,129 |
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
- FIGLA
- Protein
- p.Arg48=
- Coding
- c.142C>A
- MANE Select
- NM_001004311
- Type
- single nucleotide variant
- Location
- chr2:70790497 (GRCh38)
- Gene constraint
- LOEUF 1.279 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 71.67
Similar variants
- FIGLA p.Ala4Glu Uncertain significance ★★ ⚠ same type
- FIGLA p.Pro10His Uncertain significance ★★ ⚠ same type
- FIGLA p.Pro10Ser Uncertain significance ★★ ⚠ same type
- FIGLA p.Thr200Ile Uncertain significance ★★ ⚠ same type
- FIGLA p.Val25Met Uncertain significance ★★ ⚠ same type
- FIGLA c.231+24T>C Benign ★★ same type
- FIGLA c.384+55A>G Benign ★★ same type
- FIGLA c.610-175G>A Likely benign ★★ 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/figla-p-arg48 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown