Is MLYCD p.Asp148fs (c.443del) pathogenic?

MLYCD p.Asp148fs (c.443del) is classified Likely pathogenic in MLYCD (ClinVar, Single submitter, 1 submitter; last evaluated 2024-06-13). Associated with malonic aciduria.

What condition is associated with MLYCD p.Asp148fs (c.443del)?

MLYCD p.Asp148fs (c.443del) is associated with malonic aciduria (ClinVar).

How is Malonic aciduria inherited?

Typically Autosomal recessive (Orphanet). A genetic counselor can assess individual risk for a family.

MLYCD p.Asp148fs

c.443del · VCV3581313

Likely pathogenic Single submitter

Classification

Likely pathogenic

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

Consequence

frameshift

predicted LoF

gnomAD v4.1

Rare

Conditions

malonic aciduria

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Consequence	frameshift	predicted loss-of-function
NMD	predicted	premature termination codon in exon 1 of 5
Splicing
SpliceAI	—	not assessed · substitutions only
Constraint at this position
Conservation	phyloP 11	GERP 1.3, phastCons 1

Predicted loss-of-function is descriptive, not an applied PVS1 code.

Variant & gene context

Gene: MLYCD
Protein: p.Asp148fs
Coding: c.443del
MANE Select: NM_012213
Type: Deletion
Location: chr16:83899587 (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 148: the 'alpha-helical domain' region; a β-strand

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

Disease context

malonic aciduria — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

For Malonic aciduria (Orphanet):

Inheritance: Autosomal recessive
Onset: Childhood

Similar variants

MLYCD p.Asp148= Benign ★★ same residue
MLYCD p.Asp148Asn Uncertain significance ★ ⚠ same residue
MLYCD p.Arg21fs Pathogenic/Likely pathogenic ★★ same condition
MLYCD p.Asn179fs Pathogenic ★ same condition
MLYCD p.Gln83fs Pathogenic ★ same condition
MLYCD p.Gly369fs Likely pathogenic ★ same condition
MLYCD p.Leu133fs Pathogenic ★ same condition
MLYCD p.Leu253fs Pathogenic ★ 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-asp148fs (accessed [today's date]).

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