Is SNAP29 p.Asp13= (c.39C>T) pathogenic?

SNAP29 p.Asp13= (c.39C>T) is classified Likely benign in SNAP29 (ClinVar, Single submitter, 1 submitter; last evaluated 2022-12-23). Absent from gnomAD v4.1.

How common is SNAP29 p.Asp13= (c.39C>T) in the general population?

SNAP29 p.Asp13= (c.39C>T) is absent from gnomAD v4.1 (gnomAD).

SNAP29 p.Asp13=

c.39C>T · rs2518502190 · VCV2823432

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Absent

absent from gnomAD v4.1

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 -4
Overall
CADD	7.726	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Absent from gnomAD v4.1. Not observed in any sequenced alleles — a rarity signal (ACMG PM2-supporting), not evidence of pathogenicity on its own.

Variant & gene context

Gene: SNAP29
Protein: p.Asp13=
Coding: c.39C>T
MANE Select: NM_004782
dbSNP: rs2518502190
Type: single nucleotide variant
Location: chr22:20859149 (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 13: the 'disordered' region

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

Similar variants

SNAP29 p.Asp13Tyr Uncertain significance ⚠ same residue
SNAP29 p.Arg85Ter Pathogenic/Likely pathogenic ★★ same type
SNAP29 p.Met1Thr Pathogenic/Likely pathogenic ★★ same type
SNAP29 c.-76G>A Uncertain significance ★★ same type
SNAP29 c.*3014C>T Uncertain significance ★★ same type
SNAP29 c.*840G>C Uncertain significance ★★ same type
SNAP29 p.Ala20Pro Uncertain significance ★★ ⚠ same type
SNAP29 p.Ala65Pro Uncertain significance ★★ ⚠ same type

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-asp13 (accessed [today's date]).

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