Is EXT2 p.Glu475= (c.1425A>G) pathogenic?

EXT2 p.Glu475= (c.1425A>G) is classified Benign/Likely benign in EXT2 (ClinVar, Multiple submitters, 3 submitters; last evaluated 2024-02-12). Rare (popmax 0.224%, sas); Associated with exostoses, multiple, type 2.

What condition is associated with EXT2 p.Glu475= (c.1425A>G)?

EXT2 p.Glu475= (c.1425A>G) is associated with exostoses, multiple, type 2 (ClinVar).

How common is EXT2 p.Glu475= (c.1425A>G) in the general population?

EXT2 p.Glu475= (c.1425A>G) is rare (popmax 0.224%, sas) (gnomAD).

How is Multiple osteochondromas inherited?

Typically Autosomal dominant (Orphanet). A genetic counselor can assess individual risk for a family.

EXT2 p.Glu475=

c.1425A>G · rs533065326 · VCV1625970

Benign/Likely benign Multiple submitters

Classification

Benign/Likely benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 3 submitters

gnomAD v4.1

Rare

rare (popmax 0.224%, sas)

Conditions

exostoses, multiple, type 2

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 1.6	GERP -3.2, phastCons 1
Overall
CADD	7.59	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.224% South Asian · 204/91,084 alleles

Filtering AF 0.199% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.189%

Overall 0.0134% 216/1,614,092 alleles · rare exomes 200/1,461,818 · genomes 16/152,274 · joint denominator

Ancestry group	Frequency	1 in
South Asiangrpmax	0.224%	446
Middle Eastern	0.033%	3,031
Remaining individualsnot grpmax-eligible	0.0128%	7,813
East Asian	0.00223%	44,882
European (non-Finnish)	8.47e-05%	1,179,986

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: EXT2
Protein: p.Glu475=
Coding: c.1425A>G
MANE Select: NM_207122
dbSNP: rs533065326
Type: single nucleotide variant
Location: chr11:44197948 (GRCh38)
Gene constraint: LOEUF 0.775 · pLI <0.01 · ClinGen HI 3/3 (gnomAD)
Structure: AlphaFold pLDDT 87.59 · 6 PDB
Residue 475: an α-helix

Full EXT2 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

exostoses, multiple, type 2 — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

For Multiple osteochondromas (Orphanet):

Inheritance: Autosomal dominant
Onset: Childhood
Prevalence: >1 / 1000 (Specific population)

Similar variants

EXT2 c.1079+1G>A Pathogenic ★★ same condition
EXT2 c.1079+1G>T Pathogenic ★★ same condition
EXT2 c.1173+1G>A Pathogenic ★★ same condition
EXT2 c.1662+1G>C Likely pathogenic ★★ same condition
EXT2 c.536+1G>A Pathogenic ★★ same condition
EXT2 c.626+1G>A Pathogenic ★★ same condition
EXT2 c.626+1G>C Pathogenic ★★ same condition
EXT2 c.626+1G>T Pathogenic/Likely pathogenic ★★ 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/ext2-p-glu475 (accessed [today's date]).

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