Is ROGDI p.Asp25= (c.75C>T) pathogenic?

ROGDI p.Asp25= (c.75C>T) is classified Likely benign in ROGDI (ClinVar, Single submitter, 1 submitter; last evaluated 2022-12-08). Very rare (popmax 8.81e-05%, nfe); Associated with amelocerebrohypohidrotic syndrome.

What condition is associated with ROGDI p.Asp25= (c.75C>T)?

ROGDI p.Asp25= (c.75C>T) is associated with amelocerebrohypohidrotic syndrome (ClinVar).

How common is ROGDI p.Asp25= (c.75C>T) in the general population?

ROGDI p.Asp25= (c.75C>T) is very rare (popmax 8.81e-05%, nfe) (gnomAD).

ROGDI p.Asp25=

c.75C>T · rs1422094179 · VCV2819379

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

very rare (popmax 8.81e-05%, nfe)

Conditions

amelocerebrohypohidrotic syndrome

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 1.7	GERP 0.24, phastCons 1
Overall
CADD	11.21	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 8.81e-05% European (non-Finnish) · 1/1,134,818 alleles

Overall 6.62e-05% 1/1,509,858 alleles · very rare exomes 1/1,357,868 · genomes 0/151,990 · 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.Asp25=
Coding: c.75C>T
MANE Select: NM_024589
dbSNP: rs1422094179
Type: single nucleotide variant
Location: chr16:4802424 (GRCh38)
Gene constraint: LOEUF 1.648 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 89.59 · 2 PDB
Residue 25: a UniProt-annotated variant site (in ktzs; uncertain significance)

Full ROGDI gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

amelocerebrohypohidrotic syndrome — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Similar variants

ROGDI p.Asp25fs Pathogenic ★ same residue
ROGDI p.Asp25Glu Uncertain significance ★ ⚠ same residue
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

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-asp25 (accessed [today's date]).

Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown