Is GALNT12 p.Pro71= (c.213G>A) pathogenic?

GALNT12 p.Pro71= (c.213G>A) is classified Likely benign in GALNT12 (ClinVar, Multiple submitters, 3 submitters; last evaluated 2023-11-14). No allele count reported in gnomAD v4.1 (AN 1,209,672); Associated with colorectal cancer, susceptibility to, 1.

What condition is associated with GALNT12 p.Pro71= (c.213G>A)?

GALNT12 p.Pro71= (c.213G>A) is associated with colorectal cancer, susceptibility to, 1 (ClinVar).

How common is GALNT12 p.Pro71= (c.213G>A) in the general population?

GALNT12 p.Pro71= (c.213G>A) is no allele count reported in gnomAD v4.1 (AN 1,209,672) (gnomAD).

GALNT12 p.Pro71=

c.213G>A · rs1364225305 · VCV2087499

Likely benign Multiple submitters

Classification

Likely benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 3 submitters

gnomAD v4.1

Not reported

no allele count reported in gnomAD v4.1 (AN 1,209,672)

Conditions

colorectal cancer, susceptibility to, 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 -3.1	GERP -2.9
Overall
CADD	7.273	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

No allele count reported in gnomAD v4.1 (AN 1,209,672). This is missing data, not an absence: the variant may or may not be present in gnomAD. Rarity (ACMG PM2) and BA1/BS1 cannot be assessed for it.

Variant & gene context

Gene: GALNT12
Protein: p.Pro71=
Coding: c.213G>A
MANE Select: NM_024642
dbSNP: rs1364225305
Type: single nucleotide variant
Location: chr9:98807911 (GRCh38)
Gene constraint: LOEUF 1.054 · pLI <0.01 · ClinGen HI 1/3 (gnomAD)
Structure: AlphaFold pLDDT 93.84 · 1 PDB
Residue 71: an α-helix

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

Disease context

colorectal cancer, susceptibility to, 1 — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Similar variants

GALNT12 p.Pro71Leu Conflicting classifications of pathogenicity ★ ⚠ same residue
GALNT12 p.Pro71Ala Uncertain significance ★ ⚠ same residue
GALNT12 p.Pro71Arg Uncertain significance ★ ⚠ same residue
GALNT12 p.Pro71Ser Uncertain significance ★ ⚠ same residue
GALNT12 p.Pro71Thr Uncertain significance ★ ⚠ same residue
GALNT12 c.918-2A>C Uncertain significance ★★ same condition
GALNT12 p.Ala148Ser Uncertain significance ★★ same condition
GALNT12 p.Ala148Val Uncertain significance ★★ ⚠ 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/galnt12-p-pro71 (accessed [today's date]).

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