Is MN1 p.Glu682Lys (c.2044G>A) pathogenic?

MN1 p.Glu682Lys (c.2044G>A) is classified Uncertain significance in MN1 (ClinVar, Single submitter, 1 submitter; last evaluated 2023-10-20). AlphaMissense: likely pathogenic (0.8008); No allele count reported in gnomAD v4.1 (AN 1,547,184).

How common is MN1 p.Glu682Lys (c.2044G>A) in the general population?

MN1 p.Glu682Lys (c.2044G>A) is no allele count reported in gnomAD v4.1 (AN 1,547,184) (gnomAD).

What do computational predictors say about MN1 p.Glu682Lys (c.2044G>A)?

AlphaMissense predicts likely pathogenic (score 0.8008) — an in-silico prediction, not a clinical call.

MN1 p.Glu682Lys

c.2044G>A · VCV3363239

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely pathogenic

0.8008 · ACMG-weighted

gnomAD v4.1

Not reported

no allele count reported in gnomAD v4.1 (AN 1,547,184)

Missense predictors

1/3 damaging

AlphaMissense, REVEL, SaProt

Computational evidence

Protein change
AlphaMissense	0.8008	likely pathogenic
REVEL	0.158	moderately benign-leaning
SaProt	LLR -7.10	tolerated
⇒ AlphaMissense calls this damaging; REVEL and SaProt do not.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 7.4	GERP 1.8, phastCons 1
Regional constraint	o/e 0.99	unconstrained · MANE · 50 kb · p 0.63 · regional, not allelic
Overall
CADD	26.6	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

No allele count reported in gnomAD v4.1 (AN 1,547,184). This is missing data, not an absence: the variant may or may not be present in gnomAD. Rarity (ACMG PM2) and BA1/BS1 cannot be assessed for it.

Variant & gene context

Gene: MN1
Protein: p.Glu682Lys
Coding: c.2044G>A
MANE Select: NM_002430
Type: single nucleotide variant
Location: chr22:27798500 (GRCh38)
Gene constraint: LOEUF 0.482 · pLI 0.99 (gnomAD)
Structure: AlphaFold pLDDT 42.47
Residue 682: a UniProt-annotated variant site (in cebalid); the 'disordered' region

Full MN1 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

MN1 p.Gln1273Ter Pathogenic ★★ same type
MN1 p.Lys455Ter Likely pathogenic ★★ same type
MN1 p.Trp1248Ter Pathogenic/Likely pathogenic ★★ same type
MN1 p.Ala38Asp Uncertain significance ★★ ⚠ same type
MN1 p.Gly1092Arg Uncertain significance ★★ ⚠ same type
MN1 p.Gly120Val Uncertain significance ★★ ⚠ same type
MN1 p.Gly161Arg Uncertain significance ★★ ⚠ same type
MN1 p.Gly613Arg 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/mn1-p-glu682lys (accessed [today's date]).

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