Is DNAI1 p.Phe504= (c.1512C>T) pathogenic?

DNAI1 p.Phe504= (c.1512C>T) is classified Likely benign in DNAI1 (ClinVar, Single submitter, 1 submitter; last evaluated 2023-11-13). Ultra-rare (popmax 0.0165%, mid); Associated with primary ciliary dyskinesia.

What condition is associated with DNAI1 p.Phe504= (c.1512C>T)?

DNAI1 p.Phe504= (c.1512C>T) is associated with primary ciliary dyskinesia (ClinVar).

How common is DNAI1 p.Phe504= (c.1512C>T) in the general population?

DNAI1 p.Phe504= (c.1512C>T) is ultra-rare (popmax 0.0165%, mid) (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.Phe504=

c.1512C>T · rs1168965747 · VCV796516

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

ultra-rare (popmax 0.0165%, mid)

Conditions

primary ciliary dyskinesia

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
REVEL	0.071	moderately benign-leaning
Splicing
SpliceAI	<0.2	no splice effect predicted · four deltas, not one · how we know
Constraint at this position
Conservation	phyloP 4.9	GERP 1.2, phastCons 1
Overall
CADD	11.74	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.0165% Middle Eastern · 1/6,062 alleles

Filtering AF 0.000365% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.000137%

Overall 0.000372% 6/1,614,146 alleles · ultra-rare exomes 6/1,461,836 · genomes 0/152,310 · joint denominator

Ancestry group	Frequency	1 in
Middle Easterngrpmax	0.0165%	6,062
Remaining individualsnot grpmax-eligible	0.0032%	31,252
South Asian	0.0022%	45,539
European (non-Finnish)	8.47e-05%	1,179,998

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.Phe504=
Coding: c.1512C>T
MANE Select: NM_012144
dbSNP: rs1168965747
Type: single nucleotide variant
Location: chr9:34513134 (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 c.1019+5G>C Pathogenic/Likely pathogenic ★★ same condition
DNAI1 c.1063+1G>A Pathogenic/Likely pathogenic ★★ same condition
DNAI1 c.1063+1G>T Pathogenic/Likely pathogenic ★★ same condition
DNAI1 c.1402-1G>A Likely pathogenic ★★ same condition
DNAI1 c.1490-2A>G Likely pathogenic ★★ same condition
DNAI1 c.1569+1G>T Pathogenic/Likely pathogenic ★★ same condition
DNAI1 c.1570-1G>T Likely pathogenic ★★ same condition
DNAI1 c.1719-1G>A 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-phe504 (accessed [today's date]).

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