Is SKI p.Pro433fs (c.1298del) pathogenic?

SKI p.Pro433fs (c.1298del) is classified Uncertain significance in SKI (ClinVar, Single submitter, 1 submitter; last evaluated 2023-10-09). No gnomAD frequency available for this variant; Associated with Shprintzen-Goldberg syndrome.

What condition is associated with SKI p.Pro433fs (c.1298del)?

SKI p.Pro433fs (c.1298del) is associated with Shprintzen-Goldberg syndrome (ClinVar).

How common is SKI p.Pro433fs (c.1298del) in the general population?

SKI p.Pro433fs (c.1298del) is no gnomAD frequency available for this variant (gnomAD).

SKI p.Pro433fs

c.1298del · rs2521484390 · VCV2767297

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

Consequence

frameshift

predicted LoF

gnomAD v4.1

Not reported

no gnomAD frequency available for this variant

Conditions

Shprintzen-Goldberg syndrome

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 4 of 7
Splicing
SpliceAI	—	not assessed · substitutions only
Constraint at this position
Conservation	phyloP 8.3	GERP 1.9, phastCons 1

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

Population frequency

dbSNP / gnomAD

No gnomAD frequency available for this variant. 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: SKI
Protein: p.Pro433fs
Coding: c.1298del
MANE Select: NM_003036
dbSNP: rs2521484390
Type: Deletion
Location: chr1:2303924 (GRCh38)
Gene constraint: LOEUF 0.809 · pLI <0.01 · ClinGen HI 0/3 (gnomAD)
Structure: AlphaFold pLDDT 67.18 · 4 PDB

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

Disease context

Shprintzen-Goldberg syndrome — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Similar variants

SKI p.Pro433Leu Uncertain significance ★★ ⚠ same residue
SKI p.Pro433Arg Conflicting classifications of pathogenicity ★ ⚠ same residue
SKI p.Leu496del Uncertain significance ★★ same condition
SKI p.Ter729ArgextTer? Uncertain significance ★★ same condition
SKI c.1474+7del Likely benign ★★ same condition
SKI p.Pro433Ser Benign/Likely benign ★★ same residue
SKI p.Asp95_Ser97del Pathogenic ★ same condition
SKI p.Leu213_Ala298del 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-pro433fs (accessed [today's date]).

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