Is MGP p.Cys79= (c.237C>T) pathogenic?

MGP p.Cys79= (c.237C>T) is classified Uncertain significance in MGP (ClinVar, Single submitter, 1 submitter; last evaluated 2018-01-13). Very rare (popmax 0.00223%, eas); Associated with Keutel syndrome.

What condition is associated with MGP p.Cys79= (c.237C>T)?

MGP p.Cys79= (c.237C>T) is associated with Keutel syndrome (ClinVar).

How common is MGP p.Cys79= (c.237C>T) in the general population?

MGP p.Cys79= (c.237C>T) is very rare (popmax 0.00223%, eas) (gnomAD).

MGP p.Cys79=

c.237C>T · rs886049106 · VCV307769

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

very rare (popmax 0.00223%, eas)

Conditions

Keutel syndrome

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 -5.9	GERP -3.9
Overall
CADD	5.84	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.00223% East Asian · 1/44,896 alleles

Filtering AF 7.9e-05% ClinGen BA1/BS1 input FAF95, joint · FAF99 5.4e-05%

Overall 0.000434% 7/1,613,894 alleles · very rare

Ancestry group	Frequency	1 in
East Asiangrpmax	0.00223%	44,896
African / African-American	0.00134%	74,866
South Asian	0.0011%	91,084
European (non-Finnish)	0.000339%	294,990

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: MGP
Protein: p.Cys79=
Coding: c.237C>T
MANE Select: NM_000900
dbSNP: rs886049106
Type: single nucleotide variant
Location: chr12:14882214 (GRCh38)
Gene constraint: LOEUF 1.63 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
Structure: AlphaFold pLDDT 82.56 · 3 PDB
Residue 79: a disulfide bond; the gla domain

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

Disease context

Keutel syndrome — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Similar variants

MGP p.Cys79Arg Uncertain significance ★ ⚠ same residue
MGP c.94+1G>A Pathogenic/Likely pathogenic ★★ same condition
MGP p.Met26Thr Uncertain significance ★★ ⚠ same condition
MGP c.-63G>A Benign ★★ same condition
MGP c.*552A>T Benign ★★ same condition
MGP p.Ala8Val Benign ★★ same condition
MGP p.Asn39His Benign/Likely benign ★★ same condition
MGP p.Asn69= Benign/Likely benign ★★ 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/mgp-p-cys79 (accessed [today's date]).

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