Is ITGA3 c.2299del pathogenic?

ITGA3 c.2299del is classified Likely pathogenic in ITGA3 (ClinVar, Single submitter, 1 submitter; last evaluated 2024-02-15). Associated with epidermolysis bullosa, junctional 7, with interstitial lung disease and nephrotic syndrome.

ITGA3 c.2299del

Q: What condition is associated with ITGA3 c.2299del?

ITGA3 c.2299del is associated with epidermolysis bullosa, junctional 7, with interstitial lung disease and nephrotic syndrome (ClinVar).

Q: How is Interstitial lung disease-nephrotic syndrome-epidermolysis bullosa syndrome inherited?

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

VCV3582280

Likely pathogenic Single submitter

Classification

Likely pathogenic

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

Conditions

epidermolysis bullosa, junctional 7, with interstitial lung disease and nephrotic syndrome

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 11	GERP 0.8, phastCons 1
Non-coding constraint	Z 2.26	1 kb window · o/e 0.84 · regional · uncalibrated

Variant & gene context

Gene: ITGA3
Coding: c.2299del
MANE Select: NM_002204
Type: Deletion
Location: chr17:50078823 (GRCh38)
Gene constraint: LOEUF 0.69 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 83.88

Full ITGA3 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

epidermolysis bullosa, junctional 7, with interstitial lung disease and nephrotic syndrome — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

For Interstitial lung disease-nephrotic syndrome-epidermolysis bullosa syndrome (Orphanet):

Inheritance: Autosomal recessive
Onset: Infancy, Neonatal

Similar variants

ITGA3 c.2401-11_2409del Likely pathogenic ★ same condition
ITGA3 c.2577_2583+13del Pathogenic ★ same condition
ITGA3 c.-3_-1del Uncertain significance ★ same condition
ITGA3 p.Pro392fs Pathogenic same condition
ITGA3 c.2070+1G>A Pathogenic ★★ same condition
ITGA3 p.Arg274Gln Likely pathogenic ★★ ⚠ same condition
ITGA3 p.Arg875Ter Likely pathogenic ★★ same condition
ITGA3 p.Pro81fs 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/itga3-c-2299del (accessed [today's date]).

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