SCRIB p.Ser1276=
c.3828C>T · rs149307154 · VCV2658912
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 3 submitters
gnomAD v4.1
Rare
rare (popmax 0.647%, eas)
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 -2.2 | GERP -2.5 |
| Overall | ||
| CADD | 2.657 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.647%
East Asian · 290/44,846 alleles
Filtering AF
0.585%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.562%
Overall
0.0509%
820/1,611,050 alleles · rare
exomes 775/1,458,740 · genomes 45/152,310 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 0.647% | 155 |
| Middle Eastern | 0.0548% | 1,824 |
| European (non-Finnish) | 0.041% | 2,436 |
| Remaining individualsnot grpmax-eligible | 0.0369% | 2,711 |
| Admixed American | 0.01% | 9,994 |
| African / African-American | 0.00667% | 15,002 |
| Finnishnot grpmax-eligible | 0.00637% | 15,691 |
| South Asian | 0.0055% | 18,191 |
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
- SCRIB
- Protein
- p.Ser1276=
- Coding
- c.3828C>T
- MANE Select
- NM_182706
- dbSNP
- rs149307154
- Type
- single nucleotide variant
- Location
- chr8:143795056 (GRCh38)
- Gene constraint
- LOEUF 0.684 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 52.33 · 42 PDB
- Residue 1276
- a modified residue (phosphoserine)
Similar variants
- SCRIB c.3120+10C>G Benign/Likely benign ★★ same type
- SCRIB c.504-9C>T Benign ★★ same type
- SCRIB p.Ala1488= Likely benign ★★ same type
- SCRIB p.Arg492= Benign ★★ same type
- SCRIB p.Asn647= Benign/Likely benign ★★ same type
- SCRIB p.Leu254= Benign ★★ same type
- SCRIB p.Phe571= Benign ★★ same type
- SCRIB p.Pro1343= Benign ★★ 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/scrib-p-ser1276 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown