Is SPAG1 p.Lys891= (c.2673G>A) pathogenic?

SPAG1 p.Lys891= (c.2673G>A) is classified Likely benign in SPAG1 (ClinVar, Single submitter, 1 submitter; last evaluated 2025-09-02). No allele count reported in gnomAD v4.1 (AN 1,600,294); Associated with primary ciliary dyskinesia 28.

What condition is associated with SPAG1 p.Lys891= (c.2673G>A)?

SPAG1 p.Lys891= (c.2673G>A) is associated with primary ciliary dyskinesia 28 (ClinVar).

How common is SPAG1 p.Lys891= (c.2673G>A) in the general population?

SPAG1 p.Lys891= (c.2673G>A) is no allele count reported in gnomAD v4.1 (AN 1,600,294) (gnomAD).

How is Primary ciliary dyskinesia inherited?

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

SPAG1 p.Lys891=

c.2673G>A · VCV3684687

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Not reported

no allele count reported in gnomAD v4.1 (AN 1,600,294)

Conditions

primary ciliary dyskinesia 28

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 1.3	GERP -0.052, phastCons 0.14
Overall
CADD	3.27	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

No allele count reported in gnomAD v4.1 (AN 1,600,294). 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: SPAG1
Protein: p.Lys891=
Coding: c.2673G>A
MANE Select: NM_003114
Type: single nucleotide variant
Location: chr8:100240914 (GRCh38)
Gene constraint: LOEUF 1.084 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 74.50 · 4 PDB

Full SPAG1 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

primary ciliary dyskinesia 28 — 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

SPAG1 c.1097-11C>G Pathogenic ★★ same condition
SPAG1 c.939+1G>A Likely pathogenic ★★ same condition
SPAG1 p.Arg697Ter Pathogenic ★★ same condition
SPAG1 p.Gln672Ter Pathogenic/Likely pathogenic ★★ same condition
SPAG1 p.Ala159Thr Uncertain significance ★★ ⚠ same condition
SPAG1 p.Ala159Val Uncertain significance ★★ ⚠ same condition
SPAG1 p.Ala642Thr Uncertain significance ★★ ⚠ same condition
SPAG1 p.Arg132His Uncertain significance ★★ ⚠ 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/spag1-p-lys891 (accessed [today's date]).

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