SCP2 p.Gln243=
c.729G>A · rs1279550018 · VCV1571887
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00133%, afr)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| REVEL | 0.018 | moderately benign-leaning |
|---|---|---|
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP 0.98 | GERP -0.26, phastCons 0.47 |
| Overall | ||
| CADD | 3.366 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00133%
African / African-American · 1/75,042 alleles
Overall
0.000124%
2/1,614,062 alleles · very rare
exomes 2/1,461,772 · genomes 0/152,290 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.00133% | 75,042 |
| European (non-Finnish) | 8.47e-05% | 1,179,965 |
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
- SCP2
- Protein
- p.Gln243=
- Coding
- c.729G>A
- MANE Select
- NM_002979
- dbSNP
- rs1279550018
- Type
- single nucleotide variant
- Location
- chr1:52978271 (GRCh38)
- Gene constraint
- LOEUF 0.944 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 92.39 · 2 PDB
Similar variants
- SCP2 c.825+1G>T Pathogenic/Likely pathogenic ★★ same type
- SCP2 p.Gln371Ter Pathogenic ★★ same type
- SCP2 p.Ala359Val Uncertain significance ★★ ⚠ same type
- SCP2 p.Ala427Gly Uncertain significance ★★ ⚠ same type
- SCP2 p.Ala46Val Uncertain significance ★★ ⚠ same type
- SCP2 p.Ala545Asp Uncertain significance ★★ same type
- SCP2 p.Arg105Cys Uncertain significance ★★ ⚠ same type
- SCP2 p.Arg13Gln 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/scp2-p-gln243 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown