SUN1 p.Ala244=
c.732C>A · rs1296402515 · VCV2657170
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 8.49e-05%, nfe)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| REVEL | 0.032 | moderately benign-leaning |
|---|---|---|
| Splicing | ||
| SpliceAI | <0.2 | no splice effect predicted · four deltas, not one · how we know |
| Constraint at this position | ||
| Conservation | phyloP -1.7 | GERP -3.8 |
| Overall | ||
| CADD | 0.846 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
8.49e-05%
European (non-Finnish) · 1/1,177,772 alleles
Overall
6.22e-05%
1/1,608,894 alleles · very rare
exomes 0/1,456,712 · genomes 1/152,182 · joint denominator
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
- SUN1
- Protein
- p.Ala244=
- Coding
- c.732C>A
- MANE Select
- NM_001130965
- dbSNP
- rs1296402515
- Type
- single nucleotide variant
- Location
- chr7:851457 (GRCh38)
- Gene constraint
- LOEUF 0.712 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 60.99 · 8 PDB
- Residue 244
- the 'syne2-binding' region; the 'emd-binding' 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-ala244 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown