SCP2 p.Ser266=
c.798G>A · rs148510961 · VCV1912995
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
ultra-rare (popmax 0.0165%, mid)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| REVEL | 0.011 | strongly benign-leaning |
|---|---|---|
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP -0.15 | GERP -3.2, phastCons 0.003 |
| Overall | ||
| CADD | 8.305 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0165%
Middle Eastern · 1/6,060 alleles
Filtering AF
0.00177%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.000891%
Overall
0.00173%
28/1,613,874 alleles · ultra-rare
exomes 28/1,461,650 · genomes 0/152,224 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Middle Easterngrpmax | 0.0165% | 6,060 |
| East Asian | 0.00669% | 14,958 |
| South Asian | 0.00329% | 30,359 |
| Admixed American | 0.00167% | 60,018 |
| European (non-Finnish) | 0.00161% | 62,096 |
| African / African-American | 0.00133% | 75,034 |
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.Ser266=
- Coding
- c.798G>A
- MANE Select
- NM_002979
- dbSNP
- rs148510961
- Type
- single nucleotide variant
- Location
- chr1:52978340 (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-ser266 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown