GNPTG p.Arg124=
c.372G>A · rs781036850 · VCV793288
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 3 submitters
gnomAD v4.1
Rare
ultra-rare (popmax 0.0493%, mid)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| REVEL | 0.026 | moderately benign-leaning |
|---|---|---|
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP -0.64 | GERP -3, phastCons 0.001 |
| Overall | ||
| CADD | 5.018 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0493%
Middle Eastern · 3/6,084 alleles
Filtering AF
0.0134%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00715%
Overall
0.00155%
25/1,611,604 alleles · ultra-rare
exomes 20/1,459,372 · genomes 5/152,232 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Middle Easterngrpmax | 0.0493% | 2,028 |
| Remaining individualsnot grpmax-eligible | 0.00642% | 15,582 |
| European (non-Finnish) | 0.00153% | 65,519 |
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.Arg124=
- Coding
- c.372G>A
- MANE Select
- NM_032520
- dbSNP
- rs781036850
- Type
- single nucleotide variant
- Location
- chr16:1362092 (GRCh38)
- Gene constraint
- LOEUF 1.369 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 80.63
- Residue 124
- the mrh domain
Similar variants
- GNPTG p.Arg124Met Uncertain significance ★ ⚠ same residue
- GNPTG p.Arg124Thr Uncertain significance ★ ⚠ 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-arg124 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown