SCTR p.Ala385=
c.1155C>T · VCV4581437
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0661%, sas)
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 -7.7 | GERP -4.1 |
| Overall | ||
| CADD | 5.308 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0661%
South Asian · 60/90,732 alleles
Filtering AF
0.0527%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0478%
Overall
0.00657%
106/1,613,104 alleles · ultra-rare
exomes 89/1,460,812 · genomes 17/152,292 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 0.0661% | 1,512 |
| Remaining individualsnot grpmax-eligible | 0.008% | 12,497 |
| African / African-American | 0.00666% | 15,005 |
| European (non-Finnish) | 0.00297% | 33,700 |
| East Asian | 0.00223% | 44,866 |
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.Ala385=
- Coding
- c.1155C>T
- MANE Select
- NM_002980
- Type
- single nucleotide variant
- Location
- chr2:119441585 (GRCh38)
- Gene constraint
- LOEUF 1.373 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 77.18 · 3 PDB
- Residue 385
- 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-ala385 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown