Is MLYCD p.Ser327Arg (c.979A>C) pathogenic?

MLYCD p.Ser327Arg (c.979A>C) is classified Likely pathogenic in MLYCD (ClinVar, Single submitter, 1 submitter; last evaluated 2024-11-06). AlphaMissense: likely pathogenic (0.9984); Absent from gnomAD v4.1.

How common is MLYCD p.Ser327Arg (c.979A>C) in the general population?

MLYCD p.Ser327Arg (c.979A>C) is absent from gnomAD v4.1 (gnomAD).

What do computational predictors say about MLYCD p.Ser327Arg (c.979A>C)?

AlphaMissense predicts likely pathogenic (score 0.9984) — an in-silico prediction, not a clinical call.

MLYCD p.Ser327Arg

c.979A>C · rs1064794623 · VCV420667

Likely pathogenic Single submitter

Classification

Likely pathogenic

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely pathogenic

0.9984 · ACMG-weighted

gnomAD v4.1

Absent

absent from gnomAD v4.1

Missense predictors

3/3 damaging

AlphaMissense, REVEL, SaProt

Computational evidence

Protein change
AlphaMissense	0.9984	likely pathogenic ✓ concordant with ClinVar · top 1% in MLYCD
REVEL	0.904	moderately pathogenic-leaning
SaProt	LLR -15.29	damaging
⇒ AlphaMissense, REVEL and SaProt all call this damaging.
Splicing
SpliceAI	<0.2	all four deltas below 0.2 · A>G here scores Δ0.31 · evaluated, not missing
Constraint at this position
Conservation	phyloP 11	GERP 1.4, phastCons 1
Regional constraint	o/e 1.38	unconstrained · MANE · 16 kb · p 1.5e-22 · regional, not allelic
Overall
CADD	25.2	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

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.Ser327Arg
Coding: c.979A>C
MANE Select: NM_012213
dbSNP: rs1064794623
Type: single nucleotide variant
Location: chr16:83914986 (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 327: the 'catalytic domain' region; a β-strand

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

Similar variants

MLYCD p.Ser187Ter Pathogenic ★★ same type
MLYCD c.*218C>A Uncertain significance ★★ same type
MLYCD p.Ala119Ser Uncertain significance ★★ ⚠ same type
MLYCD p.Ala415Thr Uncertain significance ★★ ⚠ same type
MLYCD p.Arg199Gln Uncertain significance ★★ ⚠ same type
MLYCD p.Arg235Gly Uncertain significance ★★ ⚠ same type
MLYCD p.Arg392Gln Uncertain significance ★★ ⚠ same type
MLYCD p.Arg392Trp 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/mlycd-p-ser327arg (accessed [today's date]).

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