NUS1 p.Pro60=
c.180G>A · rs1772967652 · VCV1539405
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 8.75e-05%, nfe)
Conditions
1
congenital disorder of glycosylation, type Iaa
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 2.6 | GERP 1.5, phastCons 0.97 |
| Overall | ||
| CADD | 13.75 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
8.75e-05%
European (non-Finnish) · 1/1,142,336 alleles
Overall
6.5e-05%
1/1,537,990 alleles · very rare
exomes 1/1,385,794 · genomes 0/152,196 · 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
- NUS1
- Protein
- p.Pro60=
- Coding
- c.180G>A
- MANE Select
- NM_138459
- dbSNP
- rs1772967652
- Type
- single nucleotide variant
- Location
- chr6:117675850 (GRCh38)
- Gene constraint
- LOEUF 0.182 · pLI 1.00 · ClinGen HI 3/3 (gnomAD)
- Structure
- AlphaFold pLDDT 82.01 · 9 PDB
Similar variants
- NUS1 p.Pro60Ala Uncertain significance ★ ⚠ same residue
- NUS1 p.Pro60Ser Uncertain significance ★ ⚠ same residue
- NUS1 c.415+1G>A Pathogenic/Likely pathogenic ★★ same condition
- NUS1 c.692-2A>G Likely pathogenic ★★ same condition
- NUS1 p.Arg290Cys Pathogenic/Likely pathogenic ★★ same condition
- NUS1 p.Leu240Ter Pathogenic/Likely pathogenic ★★ same condition
- NUS1 p.Ala44Thr Uncertain significance ★★ ⚠ same condition
- NUS1 p.Ala79Val Uncertain significance ★★ ⚠ same condition
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/nus1-p-pro60 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown