Is SNCAIP p.Ser910Tyr (c.2729C>A) pathogenic?

SNCAIP p.Ser910Tyr (c.2729C>A) is classified Uncertain significance in SNCAIP (ClinVar, Single submitter, 1 submitter; last evaluated 2018-01-12). AlphaMissense: likely benign (0.139); Absent from gnomAD v4.1; Associated with Parkinson Disease, Dominant/Recessive.

What condition is associated with SNCAIP p.Ser910Tyr (c.2729C>A)?

SNCAIP p.Ser910Tyr (c.2729C>A) is associated with Parkinson Disease, Dominant/Recessive (ClinVar).

How common is SNCAIP p.Ser910Tyr (c.2729C>A) in the general population?

SNCAIP p.Ser910Tyr (c.2729C>A) is absent from gnomAD v4.1 (gnomAD).

What do computational predictors say about SNCAIP p.Ser910Tyr (c.2729C>A)?

AlphaMissense predicts likely benign (score 0.139) — an in-silico prediction, not a clinical call.

SNCAIP p.Ser910Tyr

c.2729C>A · rs1783693013 · VCV905322

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.139 · ACMG-weighted

gnomAD v4.1

Absent

absent from gnomAD v4.1

Missense predictors

1/3 damaging

AlphaMissense, REVEL, SaProt

Conditions

Parkinson Disease, Dominant/Recessive

Computational evidence

Protein change
AlphaMissense	0.139	likely benign
REVEL	0.037	moderately benign-leaning
SaProt	LLR -10.17	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 1.4	GERP -1.4, phastCons 0.99
Regional constraint	o/e 0.89	unconstrained · MANE · 72 kb · p 0.00024 · regional, not allelic
Overall
CADD	13.97	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: SNCAIP
Protein: p.Ser910Tyr
Coding: c.2729C>A
MANE Select: NM_005460
dbSNP: rs1783693013
Type: single nucleotide variant
Location: chr5:122451576 (GRCh38)
Gene constraint: LOEUF 0.636 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 51.98 · 1 PDB
Residue 910: the 'disordered' region

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

Disease context

Parkinson Disease, Dominant/Recessive

Similar variants

SNCAIP p.Ala363Thr Uncertain significance ★★ ⚠ same condition
SNCAIP p.Glu237Lys Uncertain significance ★★ ⚠ same condition
SNCAIP p.Leu148= Uncertain significance ★★ same condition
SNCAIP p.Ser912Arg Uncertain significance ★★ ⚠ same condition
SNCAIP c.*103C>T Likely benign ★★ same condition
SNCAIP c.*46T>G Likely benign ★★ same condition
SNCAIP c.*70C>G Benign/Likely benign ★★ same condition
SNCAIP p.Arg621Cys Likely benign ★★ 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/sncaip-p-ser910tyr (accessed [today's date]).

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