GNPTG p.Pro154=
c.462G>A · rs780619430 · VCV1101015
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
ultra-rare (popmax 0.0533%, amr)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| REVEL | 0.044 | moderately benign-leaning |
|---|---|---|
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP -6.8 | GERP -3.3 |
| Overall | ||
| CADD | 0.272 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0533%
Admixed American · 32/60,014 alleles
Filtering AF
0.0387%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0339%
Overall
0.00477%
77/1,613,360 alleles · ultra-rare
exomes 68/1,461,120 · genomes 9/152,240 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Admixed Americangrpmax | 0.0533% | 1,875 |
| Finnishnot grpmax-eligible | 0.00789% | 12,677 |
| Remaining individualsnot grpmax-eligible | 0.0064% | 15,618 |
| African / African-American | 0.00534% | 18,734 |
| South Asian | 0.00329% | 30,365 |
| European (non-Finnish) | 0.00246% | 40,689 |
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.Pro154=
- Coding
- c.462G>A
- MANE Select
- NM_032520
- dbSNP
- rs780619430
- Type
- single nucleotide variant
- Location
- chr16:1362256 (GRCh38)
- Gene constraint
- LOEUF 1.369 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 80.63
- Residue 154
- the mrh domain
Similar variants
- GNPTG p.Pro154Leu Uncertain significance ★ ⚠ same residue
- GNPTG p.Pro154fs Pathogenic/Likely pathogenic ★★ same residue
- GNPTG c.179-1G>A Likely pathogenic ★★ same type
- GNPTG c.233+1G>A Pathogenic/Likely pathogenic ★★ same type
- GNPTG c.234-1G>A Pathogenic/Likely pathogenic ★★ same type
- GNPTG c.234-1G>C Pathogenic ★★ same type
- GNPTG c.318-1G>A Pathogenic ★★ same type
- GNPTG c.52+1G>C Likely pathogenic ★★ 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/gnptg-p-pro154 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown