SUN1 p.Phe424Cys
c.1271T>G · VCV4177757
Uncertain significance
Single submitter
Classification
Uncertain significance
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00167%, amr)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| REVEL | 0.082 | moderately benign-leaning |
|---|---|---|
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP -1.5 | GERP 0.78 |
| Regional constraint | o/e 1.09 | unconstrained · MANE · 28 kb · p 0.01 · regional, not allelic |
| Overall | ||
| CADD | 12.41 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00167%
Admixed American · 1/59,734 alleles
Filtering AF
0.000429%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.000313%
Overall
0.000753%
11/1,460,530 alleles · very rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Admixed Americangrpmax | 0.00167% | 59,734 |
| European (non-Finnish) | 0.000848% | 117,948 |
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.Phe424Cys
- Coding
- c.1271T>G
- MANE Select
- NM_001130965
- Type
- single nucleotide variant
- Location
- chr7:854927 (GRCh38)
- Gene constraint
- LOEUF 0.712 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 60.99 · 8 PDB
Similar variants
- SUN1 p.Phe424Leu Uncertain significance ★ same residue
- SUN1 p.Phe424= Likely benign ★ same residue
- 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
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-phe424cys (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown