SCTR p.Ala213=
c.639G>A · rs376416323 · VCV717175
Benign
Single submitter
Classification
Benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
rare (popmax 0.453%, amr)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation/SpliceAI carries the signal. | ||
| Splicing | ||
| SpliceAI | Δ0.85 | acceptor gain · deltas |
|---|---|---|
| Pangolin | Δ0.20 | gain · loss 0.02 · agrees with SpliceAI · independent |
| Constraint at this position | ||
| Conservation | phyloP 1.1 | GERP 2.1, phastCons 0.93 |
| Overall | ||
| CADD | 22.2 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.453%
Admixed American · 265/58,442 alleles
Filtering AF
0.409%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.391%
Overall
0.0205%
328/1,598,800 alleles · rare
exomes 283/1,446,524 · genomes 45/152,276 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Admixed Americangrpmax | 0.453% | 221 |
| Remaining individualsnot grpmax-eligible | 0.0502% | 1,993 |
| African / African-American | 0.00806% | 12,402 |
| South Asian | 0.00565% | 17,685 |
| European (non-Finnish) | 0.00179% | 55,809 |
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
- SCTR
- Protein
- p.Ala213=
- Coding
- c.639G>A
- MANE Select
- NM_002980
- dbSNP
- rs376416323
- Type
- single nucleotide variant
- Location
- chr2:119461998 (GRCh38)
- Gene constraint
- LOEUF 1.373 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 77.18 · 3 PDB
- Residue 213
- an α-helix
Similar variants
- SCTR c.851+10C>T Benign ★★ same type
- SCTR p.Ala292Thr Likely benign ★★ same type
- SCTR p.Asp110Asn Benign ★★ same type
- SCTR p.Cys208= Benign ★★ same type
- SCTR p.Leu190= Benign ★★ same type
- SCTR p.Pro415= Benign ★★ same type
- SCTR p.Ala245Thr Uncertain significance ★ ⚠ same type
- SCTR p.Ala375Val 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/sctr-p-ala213 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown