SIN3A p.Arg471Ter
c.1411C>T · rs971198723 · VCV1805544
Pathogenic
Multiple submitters
Classification
Pathogenic
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 4 submitters
Consequence
nonsense (stop-gain)
predicted LoF
gnomAD v4.1
Absent
absent from gnomAD v4.1
Conditions
2
SIN3A-related intellectual disability syndrome
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Consequence | nonsense (stop-gain) | predicted loss-of-function in a haploinsufficient gene (ClinGen) |
|---|---|---|
| NMD | predicted | premature termination codon in exon 10 of 21 |
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP 12 | GERP 1.8, phastCons 1 |
| Overall | ||
| CADD | 46.0 | PHRED · no single calibrated threshold — expert panels disagree |
Predicted loss-of-function is descriptive, not an applied PVS1 code.
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
- SIN3A
- Protein
- p.Arg471Ter
- Coding
- c.1411C>T
- MANE Select
- NM_001145358
- dbSNP
- rs971198723
- Type
- single nucleotide variant
- Location
- chr15:75401967 (GRCh38)
- Gene constraint
- LOEUF 0.14 · pLI 1.00 · ClinGen HI 3/3 (gnomAD)
- Structure
- AlphaFold pLDDT 69.67
- Residue 471
- the 'interaction with sap30' region; the pah 3 domain; the 'interaction with rest' region
Similar variants
- SIN3A p.Arg471Gln Uncertain significance ★★ ⚠ same residue
- SIN3A p.Arg1140Ter Pathogenic ★★ same condition
- SIN3A p.Arg553Ter Pathogenic/Likely pathogenic ★★ same condition
- SIN3A p.Arg718Ter Pathogenic/Likely pathogenic ★★ same condition
- SIN3A p.Arg935Ter Pathogenic/Likely pathogenic ★★ same condition
- SIN3A p.Arg1205His Uncertain significance ★★ same condition
- SIN3A p.Gly733Arg Uncertain significance ★★ ⚠ same condition
- SIN3A p.Gly829Arg Uncertain significance ★★ ⚠ 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/sin3a-p-arg471ter (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown