SIN3B p.Arg203Pro
c.608G>C · VCV4538867
Uncertain significance
Single submitter
Classification
Uncertain significance
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
AlphaMissense
ambiguous
0.4026 · ACMG-weighted
gnomAD v4.1
Absent
absent from gnomAD v4.1
Missense predictors
0/2 damaging
REVEL, SaProt · AlphaMissense indeterminate
Computational evidence
| Protein change | ||
| AlphaMissense | 0.4026 | ambiguous |
|---|---|---|
| REVEL | 0.153 | moderately benign-leaning |
| SaProt | LLR -6.74 | tolerated |
| ⇒ REVEL and SaProt both call this tolerated; AlphaMissense is indeterminate. | ||
| Splicing | ||
| SpliceAI | <0.2 | no splice effect predicted · four deltas, not one · how we know |
| Constraint at this position | ||
| Conservation | phyloP 12 | GERP 2.2, phastCons 1 |
| Regional constraint | o/e 0.75 | unconstrained · MANE · 33 kb · p 7e-09 · regional, not allelic |
| Overall | ||
| CADD | 28.9 | PHRED · no single calibrated threshold — expert panels disagree |
AlphaMissense carries the ACMG weight for missense; REVEL and SaProt are independent agreement signals.
Population frequency
gnomAD v4.1 · exomes + genomes
Absent from gnomAD v4.1. Not observed in any sequenced alleles — a rarity signal (ACMG PM2-supporting), not evidence of pathogenicity on its own.
Variant & gene context
- Gene
- SIN3B
- Protein
- p.Arg203Pro
- Coding
- c.608G>C
- MANE Select
- NM_001297595
- Type
- single nucleotide variant
- Location
- chr19:16846995 (GRCh38)
- Gene constraint
- LOEUF 0.245 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 69.07 · 4 PDB
- Residue 203
- the pah 2 domain; the 'interaction with cry1' region
Similar variants
- SIN3B p.Ala534Thr Uncertain significance ★★ same type
- SIN3B p.Glu258Asp Uncertain significance ★★ ⚠ same type
- SIN3B p.His91Tyr Uncertain significance ★★ ⚠ same type
- SIN3B p.Pro281Ala Uncertain significance ★★ ⚠ same type
- SIN3B p.Val160Met Uncertain significance ★★ ⚠ same type
- SIN3B p.Val873Ile Uncertain significance ★★ ⚠ same type
- SIN3B c.1266+354G>A Benign ★★ same type
- SIN3B c.2954+6A>G 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/sin3b-p-arg203pro (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown