SUN1 p.Ala577Thr
c.1729G>A · rs2488105762 · VCV3172113
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Absent
absent from gnomAD v4.1
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| REVEL | 0.06 | moderately benign-leaning |
|---|---|---|
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP -0.23 | GERP -3.4 |
| Regional constraint | o/e 1.09 | unconstrained · MANE · 28 kb · p 0.01 · regional, not allelic |
| Overall | ||
| CADD | 0.984 | PHRED · no single calibrated threshold — expert panels disagree |
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
- SUN1
- Protein
- p.Ala577Thr
- Coding
- c.1729G>A
- MANE Select
- NM_001130965
- dbSNP
- rs2488105762
- Type
- single nucleotide variant
- Location
- chr7:860332 (GRCh38)
- Gene constraint
- LOEUF 0.712 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 60.99 · 8 PDB
- Residue 577
- the 'sufficient for interaction with syne1 and syne2' region
Similar variants
- SUN1 p.Ala179Thr Uncertain significance ★★ same type
- SUN1 p.Ala203Thr Uncertain significance ★★ same type
- SUN1 p.Ala232Val Uncertain significance ★★ same type
- SUN1 p.Ala236Thr Uncertain significance ★★ same type
- SUN1 p.Ala255Thr Uncertain significance ★★ same type
- SUN1 p.Ala256Val Uncertain significance ★★ same type
- SUN1 p.Ala404Thr Uncertain significance ★★ same type
- SUN1 p.Ala414Thr Uncertain significance ★★ 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/sun1-p-ala577thr (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown