AUTS2 p.Ser409=
c.1227C>T · rs1465863120 · VCV2804431
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Not reported
no allele count reported in gnomAD v4.1 (AN 741,500)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP 3 | GERP 2.2, phastCons 1 |
| Overall | ||
| CADD | 14.38 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
No allele count reported in gnomAD v4.1 (AN 741,500). This is missing data, not an absence: the variant may or may not be present in gnomAD. Rarity (ACMG PM2) and BA1/BS1 cannot be assessed for it.
Variant & gene context
- Gene
- AUTS2
- Protein
- p.Ser409=
- Coding
- c.1227C>T
- MANE Select
- NM_015570
- dbSNP
- rs1465863120
- Type
- single nucleotide variant
- Location
- chr7:70764764 (GRCh38)
- Gene constraint
- LOEUF 0.232 · pLI 1.00 · ClinGen HI 3/3 (gnomAD)
- Structure
- AlphaFold pLDDT 41.89
- Residue 409
- the 'important for regulation of lamellipodia formation' region; the 'disordered' region
Similar variants
- AUTS2 p.Ser409Arg Uncertain significance ★ ⚠ same residue
- AUTS2 p.Ser409_Ser410insArgSer Uncertain significance ★ same residue
- AUTS2 c.2005-1G>C Likely pathogenic ★★ same type
- AUTS2 c.742+1G>A Pathogenic ★★ same type
- AUTS2 p.Arg126Ter Pathogenic/Likely pathogenic ★★ same type
- AUTS2 p.Arg152Ter Pathogenic/Likely pathogenic ★★ same type
- AUTS2 p.Arg316Ter Pathogenic/Likely pathogenic ★★ same type
- AUTS2 p.Arg495Ter Pathogenic ★★ 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/auts2-p-ser409 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown