Is GALM p.Lys85= (c.255A>G) pathogenic?

GALM p.Lys85= (c.255A>G) is classified Likely benign in GALM (ClinVar, Single submitter, 1 submitter; last evaluated 2024-10-21). Absent from gnomAD v4.1.

How common is GALM p.Lys85= (c.255A>G) in the general population?

GALM p.Lys85= (c.255A>G) is absent from gnomAD v4.1 (gnomAD).

GALM p.Lys85=

c.255A>G · VCV3695784

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Absent

absent from gnomAD v4.1

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 2.5	GERP -2.5, phastCons 1
Overall
CADD	7.27	PHRED · no single calibrated threshold — expert panels disagree

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: GALM
Protein: p.Lys85=
Coding: c.255A>G
MANE Select: NM_138801
Type: single nucleotide variant
Location: chr2:38675976 (GRCh38)
Gene constraint: LOEUF 1.421 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 97.83 · 2 PDB
Residue 85: a UniProt-annotated variant site (in galac4; loss of protein accumulation); an α-helix

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

Similar variants

GALM p.Lys85Asn Uncertain significance ★ ⚠ same residue
GALM p.Arg131Cys Uncertain significance ★★ ⚠ same type
GALM p.Gly155Arg Uncertain significance ★★ ⚠ same type
GALM p.His333Arg Uncertain significance ★★ ⚠ same type
GALM p.Val8Met Uncertain significance ★★ ⚠ same type
GALM c.191-100G>T Benign ★★ same type
GALM c.191-128T>C Benign ★★ same type
GALM c.191-32T>A Benign ★★ 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/galm-p-lys85 (accessed [today's date]).

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