Is GALNT12 p.Ile245= (c.735C>T) pathogenic?

GALNT12 p.Ile245= (c.735C>T) is classified Likely benign in GALNT12 (ClinVar, Single submitter, 1 submitter; last evaluated 2026-02-10). Absent from gnomAD v4.1.

How common is GALNT12 p.Ile245= (c.735C>T) in the general population?

GALNT12 p.Ile245= (c.735C>T) is absent from gnomAD v4.1 (gnomAD).

GALNT12 p.Ile245=

c.735C>T · VCV4824651

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	<0.2	no splice effect predicted · four deltas, not one · how we know
Constraint at this position
Conservation	phyloP 0.78	GERP -3.8, phastCons 0.95
Overall
CADD	8.039	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: GALNT12
Protein: p.Ile245=
Coding: c.735C>T
MANE Select: NM_024642
Type: single nucleotide variant
Location: chr9:98831775 (GRCh38)
Gene constraint: LOEUF 1.054 · pLI <0.01 · ClinGen HI 1/3 (gnomAD)
Structure: AlphaFold pLDDT 93.84 · 1 PDB
Residue 245: an α-helix

Full GALNT12 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

GALNT12 p.Ile245Thr Uncertain significance ★ ⚠ same residue
GALNT12 c.1036-3C>T Uncertain significance ★★ same type
GALNT12 c.1212+1G>T Uncertain significance ★★ same type
GALNT12 c.1213-3C>T Uncertain significance ★★ same type
GALNT12 c.1344+4A>C Uncertain significance ★★ same type
GALNT12 c.732-5T>G Uncertain significance ★★ same type
GALNT12 c.918-2A>C Uncertain significance ★★ same type
GALNT12 p.Ala148Ser 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/galnt12-p-ile245 (accessed [today's date]).

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