Is MMUT p.Arg613Ser (c.1837C>A) pathogenic?

MMUT p.Arg613Ser (c.1837C>A) is classified Uncertain significance in MMUT (ClinVar, Single submitter, 1 submitter; last evaluated 2018-09-16). AlphaMissense: likely pathogenic (0.9867); Absent from gnomAD v4.1.

How common is MMUT p.Arg613Ser (c.1837C>A) in the general population?

MMUT p.Arg613Ser (c.1837C>A) is absent from gnomAD v4.1 (gnomAD).

What do computational predictors say about MMUT p.Arg613Ser (c.1837C>A)?

AlphaMissense predicts likely pathogenic (score 0.9867) — an in-silico prediction, not a clinical call.

MMUT p.Arg613Ser

c.1837C>A · rs573727541 · VCV592084

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely pathogenic

0.9867 · ACMG-weighted

gnomAD v4.1

Absent

absent from gnomAD v4.1

Missense predictors

3/3 damaging

AlphaMissense, REVEL, SaProt

Computational evidence

Protein change
AlphaMissense	0.9867	likely pathogenic
REVEL	0.865	moderately pathogenic-leaning
SaProt	LLR -13.58	damaging
⇒ AlphaMissense, REVEL and SaProt all call this damaging.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 12	GERP 2.5, phastCons 1
Regional constraint	o/e 0.94	unconstrained · MANE · 28 kb · p 0.059 · regional, not allelic
Overall
CADD	29.5	PHRED · no single calibrated threshold — expert panels disagree

ClinVar classifies this uncertain; the computational predictors unanimously lean damaging — a triage signal, not a reclassification

AlphaMissense carries the ACMG weight for missense; REVEL and SaProt are independent agreement signals.

Population frequency

gnomAD v4.1 · exomes + genomes

Absent from gnomAD v4.1. Not observed in any sequenced alleles — a rarity signal (ACMG PM2-supporting), not evidence of pathogenicity on its own.

Variant & gene context

Gene: MMUT
Protein: p.Arg613Ser
Coding: c.1837C>A
MANE Select: NM_000255
dbSNP: rs573727541
Type: single nucleotide variant
Location: chr6:49440325 (GRCh38)
Gene constraint: LOEUF 1.18 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 92.72 · 6 PDB
Residue 613: a UniProt-annotated variant site (in mamm; mut-); a UniProt-annotated variant site (in mamm; mut0)

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

Similar variants

MMUT p.Arg613Cys Likely pathogenic ★ same residue
MMUT p.Arg613Leu Likely pathogenic ★ same residue
MMUT p.Arg613= Likely benign ★ same residue
MMUT c.1083+2T>A Pathogenic ★★ same type
MMUT c.1084-10A>G Pathogenic/Likely pathogenic ★★ same type
MMUT c.1084-2A>G Pathogenic/Likely pathogenic ★★ same type
MMUT c.1445-2A>G Pathogenic/Likely pathogenic ★★ same type
MMUT c.1560+1G>T Pathogenic ★★ 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/mmut-p-arg613ser (accessed [today's date]).

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