SCTR p.Leu190=
c.568C>T · rs75071385 · VCV775755
Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
low-frequency (popmax 2.77%, afr)
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 2.7 | GERP -1.1, phastCons 1 |
| Overall | ||
| CADD | 7.816 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
2.77%
African / African-American · 2,082/75,042 alleles
Filtering AF
2.68%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 2.63%
Overall
0.161%
2,599/1,614,168 alleles · low-frequency
exomes 1,347/1,461,840 · genomes 1,252/152,328 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 2.77% | 36 |
| Ashkenazi Jewishnot grpmax-eligible | 0.446% | 224 |
| Remaining individualsnot grpmax-eligible | 0.264% | 379 |
| Middle Eastern | 0.264% | 379 |
| Admixed American | 0.22% | 455 |
| South Asian | 0.00768% | 13,013 |
| European (non-Finnish) | 0.00551% | 18,154 |
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.Leu190=
- Coding
- c.568C>T
- MANE Select
- NM_002980
- dbSNP
- rs75071385
- Type
- single nucleotide variant
- Location
- chr2:119464191 (GRCh38)
- Gene constraint
- LOEUF 1.373 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 77.18 · 3 PDB
- Residue 190
- 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.Pro415= Benign ★★ same type
- SCTR p.Ala245Thr Uncertain significance ★ ⚠ same type
- SCTR p.Ala375Val Uncertain significance ★ ⚠ same type
- SCTR p.Arg135Gln 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-leu190 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown