Is MOGS p.Asp239Asn (c.715G>A) pathogenic?

MOGS p.Asp239Asn (c.715G>A) is classified Benign/Likely benign in MOGS (ClinVar, Multiple submitters, 6 submitters; last evaluated 2026-02-04). AlphaMissense: likely benign (0.0808); Common (popmax 83.2%, eas) — too common for a highly-penetrant pathogenic allele; Associated with MOGS-congenital disorder of glycosylation.

What condition is associated with MOGS p.Asp239Asn (c.715G>A)?

MOGS p.Asp239Asn (c.715G>A) is associated with MOGS-congenital disorder of glycosylation (ClinVar).

How is MOGS-CDG inherited?

Typically Autosomal recessive (Orphanet). A genetic counselor can assess individual risk for a family.

What do computational predictors say about MOGS p.Asp239Asn (c.715G>A)?

AlphaMissense predicts likely benign (score 0.0808) — an in-silico prediction, not a clinical call.

MOGS p.Asp239Asn

Q: How common is MOGS p.Asp239Asn (c.715G>A) in the general population?

MOGS p.Asp239Asn (c.715G>A) is common (popmax 83.2%, eas) — too common for a highly-penetrant pathogenic allele (gnomAD).

c.715G>A · rs1063588 · VCV95362

Benign/Likely benign Multiple submitters

Classification

Benign/Likely benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 6 submitters

AlphaMissense

likely benign

0.0808 · ACMG-weighted

gnomAD v4.1

Common

common (popmax 83.2%, eas) — too common for a highly-penetrant pathogenic allele

Missense predictors

0/3 damaging

AlphaMissense, REVEL, SaProt

Conditions

MOGS-congenital disorder of glycosylation

Computational evidence

Protein change
AlphaMissense	0.0808	likely benign
REVEL	0.056	moderately benign-leaning
SaProt	LLR -7.04	tolerated
⇒ AlphaMissense, REVEL and SaProt all call this tolerated.
Splicing
SpliceAI	Δ0.34	donor gain · deltas
Constraint at this position
Conservation	phyloP 4.9	GERP 1.4, phastCons 1
Regional constraint	o/e 0.99	unconstrained · MANE · 2,758 bp · p 0.9 · regional, not allelic
Overall
CADD	24.6	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 83.2% East Asian · 37,340/44,860 alleles

Filtering AF 82.5% ClinGen BA1/BS1 input FAF95, joint · FAF99 82.2%

Overall 19.9% 320,491/1,613,850 alleles · common exomes 269,080/1,461,836 · genomes 51,411/152,014 · joint denominator

Ancestry group	Frequency	1 in
East Asiangrpmax	83.2%	1
African / African-American	72.8%	1
South Asian	27.9%	4
Admixed American	26.1%	4
Amishnot grpmax-eligible	23.2%	4
Remaining individualsnot grpmax-eligible	23.1%	4
Middle Eastern	18.1%	6
Finnishnot grpmax-eligible	13.9%	7
European (non-Finnish)	13.5%	7
Ashkenazi Jewishnot grpmax-eligible	12.6%	8

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.Asp239Asn
Coding: c.715G>A
MANE Select: NM_006302
dbSNP: rs1063588
Type: single nucleotide variant
Location: chr2:74463251 (GRCh38)
Gene constraint: LOEUF 0.85 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 92.42
Residue 239: a UniProt-annotated variant site (in)

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

Disease context

MOGS-congenital disorder of glycosylation — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

For MOGS-CDG (Orphanet):

Inheritance: Autosomal recessive
Onset: Infancy, Neonatal

Similar variants

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
MOGS p.Ala510Thr 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-asp239asn (accessed [today's date]).

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