Is MLYCD p.Ser382Arg (c.1146C>G) pathogenic?

MLYCD p.Ser382Arg (c.1146C>G) is classified Uncertain significance in MLYCD (ClinVar, Single submitter, 1 submitter; last evaluated 2024-11-07). AlphaMissense: likely benign (0.1854); Absent from gnomAD v4.1; Associated with Inborn genetic diseases.

What condition is associated with MLYCD p.Ser382Arg (c.1146C>G)?

MLYCD p.Ser382Arg (c.1146C>G) is associated with Inborn genetic diseases (ClinVar).

How common is MLYCD p.Ser382Arg (c.1146C>G) in the general population?

MLYCD p.Ser382Arg (c.1146C>G) is absent from gnomAD v4.1 (gnomAD).

What do computational predictors say about MLYCD p.Ser382Arg (c.1146C>G)?

AlphaMissense predicts likely benign (score 0.1854) — an in-silico prediction, not a clinical call.

MLYCD p.Ser382Arg

c.1146C>G · rs373273203 · VCV2316443

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.1854 · ACMG-weighted

gnomAD v4.1

Absent

absent from gnomAD v4.1

Missense predictors

0/2 damaging

AlphaMissense, SaProt · REVEL no call

Conditions

Inborn genetic diseases

Computational evidence

Protein change
AlphaMissense	0.1854	likely benign
REVEL	0.312	indeterminate
SaProt	LLR -6.58	tolerated
⇒ AlphaMissense and SaProt both call this tolerated; REVEL makes no call.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP -7.6	GERP -2.8
Regional constraint	o/e 1.38	unconstrained · MANE · 16 kb · p 1.5e-22 · regional, not allelic
Overall
CADD	0.871	PHRED · no single calibrated threshold — expert panels disagree

ClinVar classifies this uncertain; the computational predictors unanimously lean tolerated — 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: MLYCD
Protein: p.Ser382Arg
Coding: c.1146C>G
MANE Select: NM_012213
dbSNP: rs373273203
Type: single nucleotide variant
Location: chr16:83915153 (GRCh38)
Gene constraint: LOEUF 1.165 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
Structure: AlphaFold pLDDT 90.16 · 2 PDB
Residue 382: the 'catalytic domain' region; a turn

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

Disease context

Inborn genetic diseases — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Similar variants

MLYCD p.Ser382= Likely benign ★★ same residue
MLYCD p.Ala119Ser Uncertain significance ★★ ⚠ same condition
MLYCD p.Arg199Gln Uncertain significance ★★ ⚠ same condition
MLYCD p.Arg235Gly Uncertain significance ★★ ⚠ same condition
MLYCD p.Arg392Trp Uncertain significance ★★ ⚠ same condition
MLYCD p.Arg432Cys Uncertain significance ★★ ⚠ same condition
MLYCD p.Arg455Cys Uncertain significance ★★ ⚠ same condition
MLYCD p.Gly108Val 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/mlycd-p-ser382arg (accessed [today's date]).

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