Is MOGS p.Arg788His (c.2363G>A) pathogenic?

MOGS p.Arg788His (c.2363G>A) is classified Uncertain significance in MOGS (ClinVar, Multiple submitters, 3 submitters; last evaluated 2024-08-19). AlphaMissense: likely benign (0.1705); Very rare (popmax 0.00686%, nfe); Associated with Inborn genetic diseases.

What condition is associated with MOGS p.Arg788His (c.2363G>A)?

MOGS p.Arg788His (c.2363G>A) is associated with Inborn genetic diseases, MOGS-congenital disorder of glycosylation (ClinVar).

How common is MOGS p.Arg788His (c.2363G>A) in the general population?

MOGS p.Arg788His (c.2363G>A) is very rare (popmax 0.00686%, nfe) (gnomAD).

What do computational predictors say about MOGS p.Arg788His (c.2363G>A)?

AlphaMissense predicts likely benign (score 0.1705) — an in-silico prediction, not a clinical call.

MOGS p.Arg788His

c.2363G>A · rs199724485 · VCV964815

Uncertain significance Multiple submitters

Classification

Uncertain significance

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 3 submitters

AlphaMissense

likely benign

0.1705 · ACMG-weighted

gnomAD v4.1

Rare

very rare (popmax 0.00686%, nfe)

Missense predictors

2/3 damaging

AlphaMissense, REVEL, SaProt

Conditions

Inborn genetic diseases

Computational evidence

Protein change
AlphaMissense	0.1705	likely benign
REVEL	0.707	pathogenic-leaning
SaProt	LLR -11.51	damaging
⇒ REVEL and SaProt call this damaging; AlphaMissense does not.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 6	GERP 1.5, phastCons 1
Regional constraint	o/e 1.03	unconstrained · MANE · 601 bp · p 0.59 · regional, not allelic
Overall
CADD	27.3	PHRED · no single calibrated threshold — expert panels disagree

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

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.00686% European (non-Finnish) · 81/1,180,060 alleles

Filtering AF 0.00563% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.00515%

Overall 0.00551% 89/1,614,124 alleles · very rare exomes 85/1,461,860 · genomes 4/152,264 · joint denominator

Ancestry group	Frequency	1 in
European (non-Finnish)grpmax	0.00686%	14,569
Admixed American	0.00333%	30,007
Remaining individualsnot grpmax-eligible	0.0032%	31,244
South Asian	0.0022%	45,548
Finnishnot grpmax-eligible	0.00156%	64,014
African / African-American	0.00133%	74,944

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: MOGS
Protein: p.Arg788His
Coding: c.2363G>A
MANE Select: NM_006302
dbSNP: rs199724485
Type: single nucleotide variant
Location: chr2:74461426 (GRCh38)
Gene constraint: LOEUF 0.85 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 92.42

Full MOGS 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

Also linked: MOGS-congenital disorder of glycosylation

Similar variants

MOGS p.Arg788Cys Uncertain significance ★ ⚠ same residue
MOGS p.Arg495Ter Pathogenic/Likely pathogenic ★★ same condition
MOGS p.Gln124Ter Pathogenic ★★ same condition
MOGS p.Gln505Ter Pathogenic/Likely pathogenic ★★ same condition
MOGS p.Ala22Glu Uncertain significance ★★ ⚠ same condition
MOGS p.Ala292Asp Uncertain significance ★★ ⚠ same condition
MOGS p.Ala292Pro Uncertain significance ★★ ⚠ same condition
MOGS p.Ala41Val 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/mogs-p-arg788his (accessed [today's date]).

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