Is EXT2 c.1806+9del pathogenic?

EXT2 c.1806+9del is classified Benign/Likely benign in EXT2 (ClinVar, Multiple submitters, 2 submitters; last evaluated 2026-01-19). Ultra-rare (popmax 0.0826%, afr); Associated with exostoses, multiple, type 2.

What condition is associated with EXT2 c.1806+9del?

EXT2 c.1806+9del is associated with exostoses, multiple, type 2 (ClinVar).

How common is EXT2 c.1806+9del in the general population?

EXT2 c.1806+9del is ultra-rare (popmax 0.0826%, afr) (gnomAD).

How is Multiple osteochondromas inherited?

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

EXT2 c.1806+9del

rs372901342 · VCV465698

Benign/Likely benign Multiple submitters

Classification

Benign/Likely benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 2 submitters

gnomAD v4.1

Rare

ultra-rare (popmax 0.0826%, afr)

Conditions

exostoses, multiple, type 2

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Splicing
Splice region	donor +9	near-intronic (+9 nt from the splice site)
SpliceAI	—	not assessed · substitutions only
Constraint at this position
Conservation	phyloP 3	GERP 1.5, phastCons 1
Non-coding constraint	Z 2.10	1 kb window · o/e 0.85 · regional · uncalibrated
Overall
CADD	13.78	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.0826% African / African-American · 62/75,024 alleles

Filtering AF 0.0661% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.0602%

Overall 0.00514% 83/1,613,850 alleles · ultra-rare exomes 54/1,461,572 · genomes 29/152,278 · joint denominator

Ancestry group	Frequency	1 in
African / African-Americangrpmax	0.0826%	1,210
Middle Eastern	0.0825%	1,212
Remaining individualsnot grpmax-eligible	0.0112%	8,926
South Asian	0.00549%	18,209
Admixed American	0.00167%	60,006
European (non-Finnish)	0.000254%	393,280

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
Coding: c.1806+9del
MANE Select: NM_207122
dbSNP: rs372901342
Type: Deletion
Location: chr11:44232501 (GRCh38)
Gene constraint: LOEUF 0.775 · pLI <0.01 · ClinGen HI 3/3 (gnomAD)
Structure: AlphaFold pLDDT 87.59 · 6 PDB

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.626+2_626+5del Pathogenic ★★ same condition
EXT2 p.Gln382fs Pathogenic ★★ same condition
EXT2 p.Val593fs Likely pathogenic ★★ same condition
EXT2 p.Val68fs Pathogenic ★★ same condition
EXT2 c.2019-2del Uncertain significance ★★ same condition
EXT2 c.1080-2del Pathogenic ★ same condition
EXT2 c.1489_1495+12del Likely pathogenic ★ same condition
EXT2 c.537-4_561del 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-c-1806-plus-9del (accessed [today's date]).

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