Is EXT2 p.Phe633Ser (c.1898_1899delinsCT) pathogenic?

EXT2 p.Phe633Ser (c.18981899delinsCT) is classified Uncertain significance in EXT2 (ClinVar, Multiple submitters, 2 submitters; last evaluated 2023-08-02). No gnomAD frequency available for this variant; Associated with exostoses, multiple, type 2.

What condition is associated with EXT2 p.Phe633Ser (c.1898_1899delinsCT)?

EXT2 p.Phe633Ser (c.1898_1899delinsCT) is associated with exostoses, multiple, type 2 (ClinVar).

How common is EXT2 p.Phe633Ser (c.1898_1899delinsCT) in the general population?

EXT2 p.Phe633Ser (c.1898_1899delinsCT) is no gnomAD frequency available for this variant (gnomAD).

How is Multiple osteochondromas inherited?

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

EXT2 p.Phe633Ser

c.1898_1899delinsCT · rs2539783716 · VCV2009974

Uncertain significance Multiple submitters

Classification

Uncertain significance

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 2 submitters

gnomAD v4.1

Not reported

no gnomAD frequency available for this variant

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 · substitutions only
Constraint at this position
Conservation	phyloP 7.9	GERP 2, phastCons 1
Regional constraint	o/e 0.62	unconstrained · MANE · 37 kb · p 3.2e-09 · regional, not allelic

Population frequency

dbSNP / gnomAD

No gnomAD frequency available for this variant. 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: EXT2
Protein: p.Phe633Ser
Coding: c.1898_1899delinsCT
MANE Select: NM_207122
dbSNP: rs2539783716
Type: Indel
Location: chr11:44234206 (GRCh38)
Gene constraint: LOEUF 0.775 · pLI <0.01 · ClinGen HI 3/3 (gnomAD)
Structure: AlphaFold pLDDT 87.59 · 6 PDB
Residue 633: 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.1080-1085_1173+5684delinsGC Pathogenic ★ same condition
EXT2 p.His88fs Pathogenic ★ same condition
EXT2 p.Phe43_Gln44delinsLeuTer Pathogenic ★ same condition
EXT2 p.His601Pro Uncertain significance ★ same condition
EXT2 p.Leu177Ile Uncertain significance ★ same condition
EXT2 c.1079+1G>A Pathogenic ★★ same condition
EXT2 c.1079+1G>T Pathogenic ★★ same condition
EXT2 c.1173+1G>A 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-phe633ser (accessed [today's date]).

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