Is SNAP29 p.Val75fs (c.223del) pathogenic?

SNAP29 p.Val75fs (c.223del) is classified Pathogenic/Likely pathogenic in SNAP29 (ClinVar, Multiple submitters, 3 submitters; last evaluated 2019-06-20). No gnomAD frequency available for this variant; Associated with CEDNIK syndrome.

What condition is associated with SNAP29 p.Val75fs (c.223del)?

SNAP29 p.Val75fs (c.223del) is associated with CEDNIK syndrome (ClinVar).

How common is SNAP29 p.Val75fs (c.223del) in the general population?

SNAP29 p.Val75fs (c.223del) is no gnomAD frequency available for this variant (gnomAD).

How is CEDNIK syndrome inherited?

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

SNAP29 p.Val75fs

c.223del · rs869312906 · VCV224877

Pathogenic/Likely pathogenic Multiple submitters

Classification

Pathogenic/Likely pathogenic

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 3 submitters

Consequence

frameshift

predicted LoF

gnomAD v4.1

Not reported

no gnomAD frequency available for this variant

Conditions

CEDNIK 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 1 of 5
Splicing
SpliceAI	—	not assessed · substitutions only
Constraint at this position
Conservation	phyloP -0.83	phastCons 0.005

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: SNAP29
Protein: p.Val75fs
Coding: c.223del
MANE Select: NM_004782
dbSNP: rs869312906
Type: Deletion
Location: chr22:20859330 (GRCh38)
Gene constraint: LOEUF 0.833 · pLI 0.06 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
Structure: AlphaFold pLDDT 75.85 · 2 PDB
Residue 75: an α-helix

Full SNAP29 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

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

For CEDNIK syndrome (Orphanet):

Inheritance: Autosomal recessive
Onset: Infancy, Neonatal

Similar variants

SNAP29 p.Arg85Ter Pathogenic/Likely pathogenic ★★ same condition
SNAP29 p.Leu119fs Pathogenic/Likely pathogenic ★★ same condition
SNAP29 p.Met1Thr Pathogenic/Likely pathogenic ★★ same condition
SNAP29 p.Ser163fs Pathogenic ★★ same condition
SNAP29 c.-76G>A Uncertain significance ★★ same condition
SNAP29 c.*3014C>T Uncertain significance ★★ same condition
SNAP29 c.*840G>C Uncertain significance ★★ same condition
SNAP29 p.Arg215Cys 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/snap29-p-val75fs (accessed [today's date]).

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