Is SKI p.Ser509= (c.1527C>T) pathogenic?

SKI p.Ser509= (c.1527C>T) is classified Benign/Likely benign in SKI (ClinVar, Multiple submitters, 9 submitters; last evaluated 2026-02-01). Rare (popmax 0.876%, afr); Associated with familial thoracic aortic aneurysm and aortic dissection.

How common is SKI p.Ser509= (c.1527C>T) in the general population?

SKI p.Ser509= (c.1527C>T) is rare (popmax 0.876%, afr) (gnomAD).

SKI p.Ser509=

Q: What condition is associated with SKI p.Ser509= (c.1527C>T)?

SKI p.Ser509= (c.1527C>T) is associated with familial thoracic aortic aneurysm and aortic dissection, Shprintzen-Goldberg syndrome (ClinVar).

Q: How is Familial thoracic aortic aneurysm and aortic dissection inherited?

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

c.1527C>T · rs111935632 · VCV213674

Benign/Likely benign Multiple submitters

Classification

Benign/Likely benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 9 submitters

gnomAD v4.1

Rare

rare (popmax 0.876%, afr)

Conditions

familial thoracic aortic aneurysm and aortic dissection

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Splicing
SpliceAI	<0.2	all four deltas below 0.2 · C>A here scores Δ0.26 · evaluated, not missing
Constraint at this position
Conservation	phyloP -20	GERP -3.8
Overall
CADD	0.342	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.876% African / African-American · 641/73,148 alleles

Filtering AF 0.82% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.798%

Overall 0.0563% 873/1,551,624 alleles · rare exomes 501/1,399,324 · genomes 372/152,300 · joint denominator

Ancestry group	Frequency	1 in
African / African-Americangrpmax	0.876%	114
Remaining individualsnot grpmax-eligible	0.17%	590
Middle Eastern	0.1%	999
Admixed American	0.0941%	1,063
South Asian	0.00951%	10,510
European (non-Finnish)	0.00567%	17,645
East Asian	0.00489%	20,455
Finnishnot grpmax-eligible	0.00167%	59,816

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: SKI
Protein: p.Ser509=
Coding: c.1527C>T
MANE Select: NM_003036
dbSNP: rs111935632
Type: single nucleotide variant
Location: chr1:2304345 (GRCh38)
Gene constraint: LOEUF 0.809 · pLI <0.01 · ClinGen HI 0/3 (gnomAD)
Structure: AlphaFold pLDDT 67.18 · 4 PDB
Residue 509: the 'disordered' region

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

Disease context

familial thoracic aortic aneurysm and aortic dissection — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Also linked: Shprintzen-Goldberg syndrome

For Familial thoracic aortic aneurysm and aortic dissection (Orphanet):

Inheritance: Autosomal dominant
Onset: Adolescent, Adult, Childhood

Similar variants

SKI p.Gly116Glu Pathogenic/Likely pathogenic ★★ same condition
SKI p.Gly117Arg Pathogenic/Likely pathogenic ★★ same condition
SKI p.Gly117Ser Pathogenic/Likely pathogenic ★★ same condition
SKI p.Gly34Cys Pathogenic ★★ ⚠ same condition
SKI p.Gly34Ser Pathogenic/Likely pathogenic ★★ ⚠ same condition
SKI p.Gly34Val Pathogenic ★★ ⚠ same condition
SKI p.Leu32Val Pathogenic ★★ ⚠ same condition
SKI p.Pro35Ser 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/ski-p-ser509 (accessed [today's date]).

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