Is SNAP29 p.Thr239Pro (c.715A>C) pathogenic?

SNAP29 p.Thr239Pro (c.715A>C) is classified Uncertain significance in SNAP29 (ClinVar, Single submitter, 1 submitter; last evaluated 2021-11-05). AlphaMissense: likely benign (0.3103); Absent from gnomAD v4.1; Associated with Inborn genetic diseases.

What condition is associated with SNAP29 p.Thr239Pro (c.715A>C)?

SNAP29 p.Thr239Pro (c.715A>C) is associated with Inborn genetic diseases (ClinVar).

How common is SNAP29 p.Thr239Pro (c.715A>C) in the general population?

SNAP29 p.Thr239Pro (c.715A>C) is absent from gnomAD v4.1 (gnomAD).

What do computational predictors say about SNAP29 p.Thr239Pro (c.715A>C)?

AlphaMissense predicts likely benign (score 0.3103) — an in-silico prediction, not a clinical call.

SNAP29 p.Thr239Pro

c.715A>C · rs774151673 · VCV2258943

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.3103 · ACMG-weighted

gnomAD v4.1

Absent

absent from gnomAD v4.1

Missense predictors

1/3 damaging

AlphaMissense, REVEL, SaProt

Conditions

Inborn genetic diseases

Computational evidence

Protein change
AlphaMissense	0.3103	likely benign
REVEL	0.17	moderately benign-leaning
SaProt	LLR -10.09	damaging
⇒ SaProt calls this damaging; AlphaMissense and REVEL do not.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 6.2	GERP 0.92, phastCons 0.84
Regional constraint	o/e 1.09	unconstrained · MANE · 29 kb · p 0.086 · regional, not allelic
Overall
CADD	22.8	PHRED · no single calibrated threshold — expert panels disagree

AlphaMissense carries the ACMG weight for missense; REVEL and SaProt are independent agreement signals.

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.Thr239Pro
Coding: c.715A>C
MANE Select: NM_004782
dbSNP: rs774151673
Type: single nucleotide variant
Location: chr22:20887774 (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 239: the t-snare coiled-coil homology domain; an α-helix

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

Disease context

Inborn genetic diseases — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Similar variants

SNAP29 p.Ala20Pro Uncertain significance ★★ ⚠ same condition
SNAP29 p.Arg215Cys Uncertain significance ★★ same condition
SNAP29 p.Arg41Lys Uncertain significance ★★ ⚠ same condition
SNAP29 p.Arg83Cys Uncertain significance ★★ ⚠ same condition
SNAP29 p.Arg85Gln Uncertain significance ★★ ⚠ same condition
SNAP29 p.Asn9Ser Uncertain significance ★★ ⚠ same condition
SNAP29 p.Asp17Glu Uncertain significance ★★ ⚠ same condition
SNAP29 p.Asp232Gly 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-thr239pro (accessed [today's date]).

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