Is DNAI1 p.Ser462fs (c.1383_1384del) pathogenic?

DNAI1 p.Ser462fs (c.13831384del) is classified Pathogenic in DNAI1 (ClinVar, Single submitter, 1 submitter; last evaluated 2019-10-10). Very rare (popmax 0.0011%, sas); Associated with primary ciliary dyskinesia.

What condition is associated with DNAI1 p.Ser462fs (c.1383_1384del)?

DNAI1 p.Ser462fs (c.1383_1384del) is associated with primary ciliary dyskinesia (ClinVar).

How common is DNAI1 p.Ser462fs (c.1383_1384del) in the general population?

DNAI1 p.Ser462fs (c.1383_1384del) is very rare (popmax 0.0011%, sas) (gnomAD).

How is Primary ciliary dyskinesia inherited?

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

DNAI1 p.Ser462fs

c.1383_1384del · rs1370523337 · VCV969991

Pathogenic Single submitter

Classification

Pathogenic

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

Consequence

frameshift

predicted LoF

gnomAD v4.1

Rare

very rare (popmax 0.0011%, sas)

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 14 of 20
Splicing
SpliceAI	—	not assessed · substitutions only
Constraint at this position
Conservation	phyloP 7.9	GERP 1.9, phastCons 1

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

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.0011% South Asian · 1/91,076 alleles

Overall 6.84e-05% 1/1,461,890 alleles · very rare

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: DNAI1
Protein: p.Ser462fs
Coding: c.1383_1384del
MANE Select: NM_012144
dbSNP: rs1370523337
Type: Microsatellite
Location: chr9:34512177 (GRCh38)
Gene constraint: LOEUF 0.854 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 79.54 · 1 PDB

Full DNAI1 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

DNAI1 p.Ser462Ala Uncertain significance ★ ⚠ same residue
DNAI1 p.Phe452del Likely pathogenic ★ same condition
DNAI1 p.Pro164fs Pathogenic ★ same condition
DNAI1 p.Ser453fs Pathogenic ★ same condition
DNAI1 p.Ser547fs Pathogenic ★ same condition
DNAI1 c.501+19_501+20del Likely benign ★ same condition
DNAI1 p.Glu176del Likely benign ★ same condition
DNAI1 c.1019+5G>C 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/dnai1-p-ser462fs (accessed [today's date]).

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