NUP205 p.Pro487=
c.1461C>G · rs779026235 · VCV760701
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00331%, sas)
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 -0.74 | GERP -2.9, phastCons 0.007 |
| Overall | ||
| CADD | 7.094 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00331%
South Asian · 3/90,734 alleles
Filtering AF
0.000878%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.000444%
Overall
0.000186%
3/1,612,496 alleles · very rare
exomes 2/1,460,460 · genomes 1/152,036 · 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
- NUP205
- Protein
- p.Pro487=
- Coding
- c.1461C>G
- MANE Select
- NM_015135
- dbSNP
- rs779026235
- Type
- single nucleotide variant
- Location
- chr7:135587980 (GRCh38)
- Gene constraint
- LOEUF 0.366 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 78.46 · 5 PDB
Similar variants
- NUP205 p.Ala274Val Uncertain significance ★★ ⚠ same type
- NUP205 p.Ala2Val Uncertain significance ★★ ⚠ same type
- NUP205 p.Ala651Glu Uncertain significance ★★ ⚠ same type
- NUP205 p.Ala661Gly Uncertain significance ★★ ⚠ same type
- NUP205 p.Arg1179Cys Uncertain significance ★★ same type
- NUP205 p.Arg1206Trp Uncertain significance ★★ ⚠ same type
- NUP205 p.Arg1534His Uncertain significance ★★ ⚠ same type
- NUP205 p.Arg1591His 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/nup205-p-pro487 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown