Is GALNT2 p.Ala65= (c.195A>C) pathogenic?

GALNT2 p.Ala65= (c.195A>C) is classified Likely benign in GALNT2 (ClinVar, Single submitter, 1 submitter; last evaluated 2022-06-03). Very rare (popmax 6.2e-05%).

How common is GALNT2 p.Ala65= (c.195A>C) in the general population?

GALNT2 p.Ala65= (c.195A>C) is very rare (popmax 6.2e-05%) (gnomAD).

GALNT2 p.Ala65=

c.195A>C · rs754280873 · VCV2106945

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

very rare (popmax 6.2e-05%)

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	GERP -4.2
Overall
CADD	3.89	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 6.2e-05%

Overall 6.2e-05% 1/1,614,088 alleles · very rare exomes 1/1,461,754 · genomes 0/152,334 · joint denominator

Rarity supports pathogenicity (ACMG PM2); frequency above a disease-specific BA1/BS1 threshold argues against it. A variant frequent in one ancestry group can be near-absent in others, so a single global figure can mislead.

Variant & gene context

Gene: GALNT2
Protein: p.Ala65=
Coding: c.195A>C
MANE Select: NM_004481
dbSNP: rs754280873
Type: single nucleotide variant
Location: chr1:230178286 (GRCh38)
Gene constraint: LOEUF 0.515 · pLI 0.89 (gnomAD)
Structure: AlphaFold pLDDT 90.27 · 13 PDB
Residue 65: the 'disordered' region

Full GALNT2 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

GALNT2 p.Arg200Ter Pathogenic ★★ same type
GALNT2 c.1560+4C>T Uncertain significance ★★ same type
GALNT2 p.Ala299Thr Uncertain significance ★★ ⚠ same type
GALNT2 p.Ala30Val Uncertain significance ★★ ⚠ same type
GALNT2 p.Ala35Thr Uncertain significance ★★ ⚠ same type
GALNT2 p.Arg128Gln Uncertain significance ★★ ⚠ same type
GALNT2 p.Arg404Ile Uncertain significance ★★ ⚠ same type
GALNT2 p.Arg502Gln 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/galnt2-p-ala65 (accessed [today's date]).

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