Is DNAI1 p.Ala60Val (c.179C>T) pathogenic?

DNAI1 p.Ala60Val (c.179C>T) is classified Benign/Likely benign in DNAI1 (ClinVar, Multiple submitters, 8 submitters; last evaluated 2026-02-02). AlphaMissense: likely benign (0.1382); Common (popmax 7.57%, afr) — too common for a highly-penetrant pathogenic allele; Associated with primary ciliary dyskinesia.

What condition is associated with DNAI1 p.Ala60Val (c.179C>T)?

DNAI1 p.Ala60Val (c.179C>T) is associated with primary ciliary dyskinesia, primary ciliary dyskinesia 1 (ClinVar).

How is Primary ciliary dyskinesia inherited?

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

What do computational predictors say about DNAI1 p.Ala60Val (c.179C>T)?

AlphaMissense predicts likely benign (score 0.1382) — an in-silico prediction, not a clinical call.

DNAI1 p.Ala60Val

Q: How common is DNAI1 p.Ala60Val (c.179C>T) in the general population?

DNAI1 p.Ala60Val (c.179C>T) is common (popmax 7.57%, afr) — too common for a highly-penetrant pathogenic allele (gnomAD).

c.179C>T · rs16931549 · VCV163163

Benign/Likely benign Multiple submitters

Classification

Benign/Likely benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 8 submitters

AlphaMissense

likely benign

0.1382 · ACMG-weighted

gnomAD v4.1

Common

common (popmax 7.57%, afr) — too common for a highly-penetrant pathogenic allele

Missense predictors

0/3 damaging

AlphaMissense, REVEL, SaProt

Conditions

primary ciliary dyskinesia

Computational evidence

Protein change
AlphaMissense	0.1382	likely benign
REVEL	0.222	benign-leaning
SaProt	LLR -8.35	tolerated
⇒ AlphaMissense, REVEL and SaProt all call this tolerated.
Splicing
SpliceAI	<0.2	all four deltas below 0.2 · C>A here scores Δ0.34 · evaluated, not missing
Constraint at this position
Conservation	phyloP 2.3	GERP 0.82, phastCons 0.99
Regional constraint	o/e 0.97	unconstrained · MANE · 62 kb · p 0.35 · regional, not allelic
Overall
CADD	24.9	PHRED · no single calibrated threshold — expert panels disagree

AlphaMissense carries the ACMG weight for missense; REVEL and SaProt are independent agreement signals.

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 7.57% African / African-American · 5,678/74,994 alleles

Filtering AF 7.41% ClinGen BA1/BS1 input FAF95, joint · FAF99 7.34%

Overall 0.412% 6,647/1,614,094 alleles · common

Ancestry group	Frequency	1 in
African / African-Americangrpmax	7.57%	13
Admixed American	0.566%	177
Remaining individualsnot grpmax-eligible	0.533%	188
Middle Eastern	0.38%	263
Ashkenazi Jewishnot grpmax-eligible	0.172%	581
European (non-Finnish)	0.0178%	5,619
South Asian	0.00988%	10,120
East Asian	0.00668%	14,959

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.Ala60Val
Coding: c.179C>T
MANE Select: NM_012144
dbSNP: rs16931549
Type: single nucleotide variant
Location: chr9:34485239 (GRCh38)
Gene constraint: LOEUF 0.854 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 79.54 · 1 PDB
Residue 60: a UniProt-annotated variant site (in)

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

Also linked: primary ciliary dyskinesia 1

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.Ala60= Uncertain significance ★ same residue
DNAI1 p.Ala60Thr Uncertain significance ★ ⚠ same residue
DNAI1 p.Ala60fs Pathogenic/Likely pathogenic ★★ same residue
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

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-ala60val (accessed [today's date]).

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