Is DHDDS p.Ser79Gly (c.235A>G) pathogenic?

DHDDS p.Ser79Gly (c.235A>G) is classified Uncertain significance in DHDDS (ClinVar, Single submitter, 1 submitter; last evaluated 2025-11-26). AlphaMissense: likely pathogenic (0.9812); Absent from gnomAD v4.1; Associated with Inborn genetic diseases.

What condition is associated with DHDDS p.Ser79Gly (c.235A>G)?

DHDDS p.Ser79Gly (c.235A>G) is associated with Inborn genetic diseases (ClinVar).

How common is DHDDS p.Ser79Gly (c.235A>G) in the general population?

DHDDS p.Ser79Gly (c.235A>G) is absent from gnomAD v4.1 (gnomAD).

What do computational predictors say about DHDDS p.Ser79Gly (c.235A>G)?

AlphaMissense predicts likely pathogenic (score 0.9812) — an in-silico prediction, not a clinical call.

DHDDS p.Ser79Gly

c.235A>G · VCV4617288

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely pathogenic

0.9812 · ACMG-weighted

gnomAD v4.1

Absent

absent from gnomAD v4.1

Missense predictors

3/3 damaging

AlphaMissense, REVEL, SaProt

Conditions

Inborn genetic diseases

Computational evidence

Protein change
AlphaMissense	0.9812	likely pathogenic
REVEL	0.857	moderately pathogenic-leaning
SaProt	LLR -12.88	damaging
⇒ AlphaMissense, REVEL and SaProt all call this damaging.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 11	GERP 1.9, phastCons 1
Regional constraint	o/e 0.58	unconstrained · MANE · 9,886 bp · p 3.6e-06 · regional, not allelic
Overall
CADD	29.0	PHRED · no single calibrated threshold — expert panels disagree

ClinVar classifies this uncertain; the computational predictors unanimously lean damaging — a triage signal, not a reclassification

AlphaMissense carries the ACMG weight for missense; REVEL and SaProt are independent agreement signals.

Population frequency

gnomAD v4.1 · exomes + genomes

Absent from gnomAD v4.1. Not observed in any sequenced alleles — a rarity signal (ACMG PM2-supporting), not evidence of pathogenicity on its own.

Variant & gene context

Gene: DHDDS
Protein: p.Ser79Gly
Coding: c.235A>G
MANE Select: NM_205861
Type: single nucleotide variant
Location: chr1:26442785 (GRCh38)
Gene constraint: LOEUF 0.536 · pLI 0.91 (gnomAD)
Structure: AlphaFold pLDDT 95.01 · 9 PDB
Residue 79: a UniProt-annotated variant site (in rp59; in a patient with congenital disorder of glycosylation); a β-strand

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

Disease context

Inborn genetic diseases — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Similar variants

DHDDS p.Arg38His Pathogenic/Likely pathogenic ★★ same condition
DHDDS c.542+6C>A Uncertain significance ★★ same condition
DHDDS p.Ala316Thr Uncertain significance ★★ ⚠ same condition
DHDDS p.Arg265Trp Uncertain significance ★★ ⚠ same condition
DHDDS p.Arg298Cys Uncertain significance ★★ ⚠ same condition
DHDDS p.Arg327His Uncertain significance ★★ ⚠ same condition
DHDDS p.Arg63Trp Uncertain significance ★★ ⚠ same condition
DHDDS p.Gln140Arg Uncertain significance ★★ ⚠ 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/dhdds-p-ser79gly (accessed [today's date]).

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