Is MOGS p.Arg601Ter (c.1801C>T) pathogenic?

MOGS p.Arg601Ter (c.1801C>T) is classified Pathogenic in MOGS (ClinVar, Single submitter, 1 submitter; last evaluated 2015-03-12). Very rare (popmax 0.00223%, eas).

How common is MOGS p.Arg601Ter (c.1801C>T) in the general population?

MOGS p.Arg601Ter (c.1801C>T) is very rare (popmax 0.00223%, eas) (gnomAD).

MOGS p.Arg601Ter

c.1801C>T · rs1057520537 · VCV379238

Pathogenic Single submitter

Classification

Pathogenic

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

Consequence

nonsense (stop-gain)

predicted LoF

gnomAD v4.1

Rare

very rare (popmax 0.00223%, eas)

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Consequence	nonsense (stop-gain)	predicted loss-of-function
NMD	escapes	premature termination codon in the last exon (4 of 4) — the truncated protein is likely expressed. PVS1 input, not an applied code
Splicing
SpliceAI	<0.2	no splice effect predicted · four deltas, not one · how we know
Constraint at this position
Conservation	phyloP 0.73	GERP 0.42, phastCons 0.41
Overall
CADD	37.0	PHRED · no single calibrated threshold — expert panels disagree

Predicted loss-of-function is descriptive, not an applied PVS1 code.

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.00223% East Asian · 1/44,888 alleles

Filtering AF 0.000429% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.000312%

Overall 0.000682% 11/1,614,042 alleles · very rare exomes 10/1,461,884 · genomes 1/152,158 · joint denominator

Ancestry group	Frequency	1 in
East Asiangrpmax	0.00223%	44,888
European (non-Finnish)	0.000847%	118,002

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.Arg601Ter
Coding: c.1801C>T
MANE Select: NM_006302
dbSNP: rs1057520537
Type: single nucleotide variant
Location: chr2:74461988 (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

Similar variants

MOGS p.Arg601Gln Uncertain significance ★ ⚠ same residue
MOGS p.Arg601= Likely benign ★ same residue
MOGS p.Arg495Ter Pathogenic/Likely pathogenic ★★ same type
MOGS p.Gln124Ter Pathogenic ★★ same type
MOGS p.Gln505Ter Pathogenic/Likely pathogenic ★★ same type
MOGS p.Ala22Glu Uncertain significance ★★ ⚠ same type
MOGS p.Ala292Asp Uncertain significance ★★ ⚠ same type
MOGS p.Ala292Pro Uncertain significance ★★ ⚠ same type

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-arg601ter (accessed [today's date]).

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