Is MOGS p.Pro704= (c.2112C>T) pathogenic?

MOGS p.Pro704= (c.2112C>T) is classified Benign/Likely benign in MOGS (ClinVar, Multiple submitters, 2 submitters; last evaluated 2026-01-28). Low-frequency (popmax 2.15%, sas); Associated with MOGS-congenital disorder of glycosylation.

What condition is associated with MOGS p.Pro704= (c.2112C>T)?

MOGS p.Pro704= (c.2112C>T) is associated with MOGS-congenital disorder of glycosylation (ClinVar).

How common is MOGS p.Pro704= (c.2112C>T) in the general population?

MOGS p.Pro704= (c.2112C>T) is low-frequency (popmax 2.15%, sas) (gnomAD).

How is MOGS-CDG inherited?

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

MOGS p.Pro704=

c.2112C>T · rs561758565 · VCV465840

Benign/Likely benign Multiple submitters

Classification

Benign/Likely benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 2 submitters

gnomAD v4.1

Rare

low-frequency (popmax 2.15%, sas)

Conditions

MOGS-congenital disorder of glycosylation

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 0.032	GERP 0.62, phastCons 0.004
Overall
CADD	6.592	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 2.15% South Asian · 1,959/91,090 alleles

Filtering AF 2.07% ClinGen BA1/BS1 input FAF95, joint · FAF99 2.04%

Overall 0.128% 2,074/1,614,214 alleles · low-frequency exomes 1,950/1,461,874 · genomes 124/152,340 · joint denominator

Ancestry group	Frequency	1 in
South Asiangrpmax	2.15%	46
Remaining individualsnot grpmax-eligible	0.117%	856
Middle Eastern	0.066%	1,516
Admixed American	0.00833%	12,006
African / African-American	0.00266%	37,528
European (non-Finnish)	0.00254%	39,334
East Asian	0.00223%	44,884

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.Pro704=
Coding: c.2112C>T
MANE Select: NM_006302
dbSNP: rs561758565
Type: single nucleotide variant
Location: chr2:74461677 (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

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-pro704 (accessed [today's date]).

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