ROGDI p.Ser83=
c.249C>T · rs769659198 · VCV1620934
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00673%, amr)
Conditions
1
amelocerebrohypohidrotic syndrome
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | <0.2 | all four deltas below 0.2 · G>C here scores Δ0.29 · evaluated, not missing |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP 8.5 | GERP 1, phastCons 1 |
| Overall | ||
| CADD | 13.79 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00673%
Admixed American · 4/59,454 alleles
Filtering AF
0.00227%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00136%
Overall
0.000249%
4/1,606,618 alleles · very rare
exomes 3/1,454,438 · genomes 1/152,180 · 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
- ROGDI
- Protein
- p.Ser83=
- Coding
- c.249C>T
- MANE Select
- NM_024589
- dbSNP
- rs769659198
- Type
- single nucleotide variant
- Location
- chr16:4801273 (GRCh38)
- Gene constraint
- LOEUF 1.648 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 89.59 · 2 PDB
- Residue 83
- a β-strand
Similar variants
- ROGDI c.117+1G>A Pathogenic/Likely pathogenic ★★ same condition
- ROGDI c.46-2A>G Likely pathogenic ★★ same condition
- ROGDI c.531+5G>C Likely pathogenic ★★ same condition
- ROGDI c.645+2T>A Likely pathogenic ★★ same condition
- ROGDI p.Arg157Ter Pathogenic ★★ same condition
- ROGDI p.Gln112Ter Pathogenic/Likely pathogenic ★★ same condition
- ROGDI p.Gln114Ter Pathogenic/Likely pathogenic ★★ same condition
- ROGDI p.Gln96Ter 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/rogdi-p-ser83 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown