SUN5 p.Ala206=
c.618C>T · rs757373537 · VCV2498884
Uncertain significance
Single submitter
Classification
Uncertain significance
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0658%, mid)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation/SpliceAI carries the signal. | ||
| Splicing | ||
| SpliceAI | Δ0.31 | acceptor loss · deltas |
|---|---|---|
| Pangolin | Δ0.23 | loss · gain 0.00 · agrees with SpliceAI · independent |
| Constraint at this position | ||
| Conservation | phyloP 4 | GERP 0.1, phastCons 1 |
| Overall | ||
| CADD | 6.065 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0658%
Middle Eastern · 4/6,082 alleles
Filtering AF
0.0224%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0168%
Overall
0.00807%
130/1,611,486 alleles · ultra-rare
exomes 118/1,459,456 · genomes 12/152,030 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Middle Easterngrpmax | 0.0658% | 1,521 |
| African / African-American | 0.0294% | 3,403 |
| Remaining individualsnot grpmax-eligible | 0.0176% | 5,676 |
| Admixed American | 0.0117% | 8,536 |
| European (non-Finnish) | 0.00712% | 14,036 |
| East Asian | 0.00223% | 44,834 |
| South Asian | 0.00111% | 90,152 |
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
- SUN5
- Protein
- p.Ala206=
- Coding
- c.618C>T
- MANE Select
- NM_080675
- dbSNP
- rs757373537
- Type
- single nucleotide variant
- Location
- chr20:32987771 (GRCh38)
- Gene constraint
- LOEUF 1.146 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 75.31
- Residue 206
- a UniProt-annotated variant site (in spgf16; in mouse model abolishes interaction with dnajb13); the sun domain
Similar variants
- SUN5 p.Arg356Cys Likely pathogenic ★★ same type
- SUN5 p.Arg149Ter Likely pathogenic ★ same type
- SUN5 c.984+8C>T Uncertain significance ★ same type
- SUN5 p.Ala28Ser Uncertain significance ★ ⚠ same type
- SUN5 p.Ala364Ser Uncertain significance ★ ⚠ same type
- SUN5 p.Ala59Thr Uncertain significance ★ ⚠ same type
- SUN5 p.Ala84Val Uncertain significance ★ ⚠ same type
- SUN5 p.Arg30Gln 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/sun5-p-ala206 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown