SCRIB p.Thr400=
c.1200G>A · rs762494915 · VCV3046359
Likely benign
No assertion criteria
Classification
Likely benign
ClinVar
Review
No assertion criteria ☆☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00568%, nfe)
Conditions
1
SCRIB-related disorder
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | <0.2 | no splice effect predicted · four deltas, not one · how we know |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP -16 | GERP -4 |
| Overall | ||
| CADD | 0.099 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00568%
European (non-Finnish) · 67/1,179,416 alleles
Filtering AF
0.00454%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00417%
Overall
0.00441%
71/1,611,392 alleles · very rare
exomes 68/1,459,142 · genomes 3/152,250 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| European (non-Finnish)grpmax | 0.00568% | 17,603 |
| South Asian | 0.0033% | 30,295 |
| Remaining individualsnot grpmax-eligible | 0.0016% | 62,332 |
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.Thr400=
- Coding
- c.1200G>A
- MANE Select
- NM_182706
- dbSNP
- rs762494915
- Type
- single nucleotide variant
- Location
- chr8:143810979 (GRCh38)
- Gene constraint
- LOEUF 0.684 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 52.33 · 42 PDB
- Residue 400
- the 'sufficient for targeting to adherens junction and to inhibit cell proliferation' region
Disease context
SCRIB-related disorder
Similar variants
- SCRIB p.Arg231Gln Uncertain significance ★ ⚠ same condition
- SCRIB c.2179-10C>T Likely benign same condition
- SCRIB c.3714+7G>A Likely benign same condition
- SCRIB c.4018-6C>T Likely benign same condition
- SCRIB c.4514+8C>T Likely benign same condition
- SCRIB c.4515-4G>A Likely benign same condition
- SCRIB c.907-4C>G Likely benign same condition
- SCRIB c.907-4C>T Likely benign same condition
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-thr400 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown