Is ITGA3 p.Asp865fs (c.2593del) pathogenic?

ITGA3 p.Asp865fs (c.2593del) is classified Likely pathogenic in ITGA3 (ClinVar, No assertion criteria, 1 submitter; last evaluated 2017-11-10). Very rare (popmax 0.00119%, sas); Associated with nephrotic syndrome.

What condition is associated with ITGA3 p.Asp865fs (c.2593del)?

ITGA3 p.Asp865fs (c.2593del) is associated with nephrotic syndrome (ClinVar).

How common is ITGA3 p.Asp865fs (c.2593del) in the general population?

ITGA3 p.Asp865fs (c.2593del) is very rare (popmax 0.00119%, sas) (gnomAD).

ITGA3 p.Asp865fs

c.2593del · rs2144304926 · VCV1344695

Likely pathogenic No assertion criteria

Classification

Likely pathogenic

ClinVar

Review

No assertion criteria ☆☆☆☆

ClinVar · 1 submitter

Consequence

frameshift

predicted LoF

gnomAD v4.1

Rare

very rare (popmax 0.00119%, sas)

Conditions

nephrotic syndrome

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Consequence	frameshift	predicted loss-of-function
NMD	predicted	premature termination codon in exon 21 of 26
Splicing
SpliceAI	—	not assessed · substitutions only
Constraint at this position
Conservation	phyloP -1.9	GERP -3.6

Predicted loss-of-function is descriptive, not an applied PVS1 code.

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.00119% South Asian · 1/83,700 alleles

Overall 6.4e-05% 1/1,562,694 alleles · very rare exomes 1/1,410,380 · genomes 0/152,314 · joint denominator

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: ITGA3
Protein: p.Asp865fs
Coding: c.2593del
MANE Select: NM_002204
dbSNP: rs2144304926
Type: Deletion
Location: chr17:50079441 (GRCh38)
Gene constraint: LOEUF 0.69 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 83.88
Residue 865: the 'disordered' region

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

Disease context

nephrotic syndrome — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Similar variants

ITGA3 p.Arg628Pro Pathogenic/Likely pathogenic ⚠ same condition
ITGA3 c.2299del Likely pathogenic ★ same type
ITGA3 c.2401-11_2409del Likely pathogenic ★ same type
ITGA3 c.2577_2583+13del Pathogenic ★ same type
ITGA3 c.-3_-1del Uncertain significance ★ same type
ITGA3 c.2297+255del Benign ★ same type
ITGA3 c.2821-85del Benign ★ same type
ITGA3 c.*479del Benign ★ same type

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-p-asp865fs (accessed [today's date]).

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