Is DNAI2 p.Arg459fs (c.1375del) pathogenic?

DNAI2 p.Arg459fs (c.1375del) is classified Pathogenic in DNAI2 (ClinVar, Single submitter, 1 submitter; last evaluated 2021-10-03). Absent from gnomAD; Associated with primary ciliary dyskinesia.

What condition is associated with DNAI2 p.Arg459fs (c.1375del)?

DNAI2 p.Arg459fs (c.1375del) is associated with primary ciliary dyskinesia (ClinVar).

How common is DNAI2 p.Arg459fs (c.1375del) in the general population?

DNAI2 p.Arg459fs (c.1375del) is absent from gnomAD (gnomAD).

How is Primary ciliary dyskinesia inherited?

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

DNAI2 p.Arg459fs

c.1375del · rs2144112583 · VCV1456236

Pathogenic Single submitter

Classification

Pathogenic

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

Consequence

frameshift

predicted LoF

gnomAD v4.1

Not reported

no gnomAD frequency available for this variant

Conditions

primary ciliary dyskinesia

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 11 of 14
Splicing
SpliceAI	—	not assessed · substitutions only
Constraint at this position
Conservation	phyloP 6	GERP 1.5, phastCons 1

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

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: DNAI2
Protein: p.Arg459fs
Coding: c.1375del
MANE Select: NM_023036
dbSNP: rs2144112583
Type: Deletion
Location: chr17:74310043 (GRCh38)
Gene constraint: LOEUF 0.966 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
Structure: AlphaFold pLDDT 84.27 · 1 PDB

Full DNAI2 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

primary ciliary dyskinesia — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

For Primary ciliary dyskinesia (Orphanet):

Inheritance: Autosomal dominant, Autosomal recessive, X-linked recessive
Onset: Neonatal
Prevalence: 1-5 / 10 000 (Pakistan)

Similar variants

DNAI2 p.Arg459Trp Uncertain significance ★★ ⚠ same residue
DNAI2 p.Arg459Gln Uncertain significance ★ ⚠ same residue
DNAI2 p.Asn45fs Pathogenic/Likely pathogenic ★★ same condition
DNAI2 p.Asp84fs Pathogenic/Likely pathogenic ★★ same condition
DNAI2 p.Phe375fs Pathogenic/Likely pathogenic ★★ same condition
DNAI2 p.Thr475fs Pathogenic/Likely pathogenic ★★ same condition
DNAI2 c.1211+2_1211+5del Likely pathogenic ★ same condition
DNAI2 c.1212-17_1250del 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/dnai2-p-arg459fs (accessed [today's date]).

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