Is GALNT2 p.Arg210= (c.630G>A) pathogenic?

GALNT2 p.Arg210= (c.630G>A) is classified Likely benign in GALNT2 (ClinVar, Single submitter, 1 submitter; last evaluated 2025-10-19). Rare (popmax 0.514%, eas).

How common is GALNT2 p.Arg210= (c.630G>A) in the general population?

GALNT2 p.Arg210= (c.630G>A) is rare (popmax 0.514%, eas) (gnomAD).

GALNT2 p.Arg210=

c.630G>A · VCV3711710

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

rare (popmax 0.514%, eas)

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 0.13	GERP -3.9, phastCons 0.83
Overall
CADD	5.59	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.514% East Asian · 230/44,708 alleles

Filtering AF 0.46% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.439%

Overall 0.0147% 236/1,608,152 alleles · rare exomes 226/1,455,790 · genomes 10/152,362 · joint denominator

Ancestry group	Frequency	1 in
East Asiangrpmax	0.514%	194
Middle Eastern	0.0165%	6,054
Remaining individualsnot grpmax-eligible	0.0032%	31,212
European (non-Finnish)	0.000254%	393,042

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.Arg210=
Coding: c.630G>A
MANE Select: NM_004481
Type: single nucleotide variant
Location: chr1:230243328 (GRCh38)
Gene constraint: LOEUF 0.515 · pLI 0.89 (gnomAD)
Structure: AlphaFold pLDDT 90.27 · 13 PDB
Residue 210: a UniProt-annotated variant site (in cdg2t; loss of apoc-iii glycosylation); an α-helix; the 'catalytic subdomain a' region

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

Similar variants

GALNT2 p.Arg210Pro Likely pathogenic ★ same residue
GALNT2 p.Arg210Gln Uncertain significance ★ ⚠ same residue
GALNT2 p.Arg210Trp Uncertain significance ★ same residue
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

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-arg210 (accessed [today's date]).

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