GNPTG p.Pro85=
c.255G>A · rs76594024 · VCV317881
Benign/Likely benign
Multiple submitters
Classification
Benign/Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 9 submitters
gnomAD v4.1
Rare
low-frequency (popmax 1.04%, nfe)
Conditions
1
GNPTG-mucolipidosis
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| REVEL | 0.089 | moderately benign-leaning |
|---|---|---|
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP -11 | GERP -3 |
| Overall | ||
| CADD | 0.258 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
1.04%
European (non-Finnish) · 12,229/1,180,038 alleles
Filtering AF
1.02%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 1.01%
Overall
0.829%
13,375/1,613,808 alleles · low-frequency
exomes 12,492/1,461,466 · genomes 883/152,342 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| European (non-Finnish)grpmax | 1.04% | 96 |
| Remaining individualsnot grpmax-eligible | 0.658% | 152 |
| Admixed American | 0.466% | 214 |
| African / African-American | 0.252% | 397 |
| Ashkenazi Jewishnot grpmax-eligible | 0.236% | 423 |
| South Asian | 0.13% | 772 |
| Finnishnot grpmax-eligible | 0.112% | 896 |
| Middle Eastern | 0.099% | 1,010 |
| East Asian | 0.00223% | 44,882 |
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
- GNPTG
- Protein
- p.Pro85=
- Coding
- c.255G>A
- MANE Select
- NM_032520
- dbSNP
- rs76594024
- Type
- single nucleotide variant
- Location
- chr16:1361893 (GRCh38)
- Gene constraint
- LOEUF 1.369 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 80.63
- Residue 85
- the mrh domain
Similar variants
- GNPTG p.Pro85Leu Uncertain significance ★★ same residue
- GNPTG c.179-1G>A Likely pathogenic ★★ same condition
- GNPTG c.233+1G>A Pathogenic/Likely pathogenic ★★ same condition
- GNPTG c.234-1G>A Pathogenic/Likely pathogenic ★★ same condition
- GNPTG c.234-1G>C Pathogenic ★★ same condition
- GNPTG c.318-1G>A Pathogenic ★★ same condition
- GNPTG c.52+1G>C Likely pathogenic ★★ same condition
- GNPTG c.526+2T>G Likely pathogenic ★★ 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/gnptg-p-pro85 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown