Is DYTN p.Ser202Pro (c.604T>C) pathogenic?

DYTN p.Ser202Pro (c.604T>C) is classified Uncertain significance in DYTN (ClinVar, Single submitter, 1 submitter; last evaluated 2023-11-18). AlphaMissense: ambiguous (0.5467); Absent from gnomAD v4.1.

How common is DYTN p.Ser202Pro (c.604T>C) in the general population?

DYTN p.Ser202Pro (c.604T>C) is absent from gnomAD v4.1 (gnomAD).

What do computational predictors say about DYTN p.Ser202Pro (c.604T>C)?

AlphaMissense predicts ambiguous (score 0.5467) — an in-silico prediction, not a clinical call.

DYTN p.Ser202Pro

c.604T>C · rs1699957886 · VCV3086656

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

ambiguous

0.5467 · ACMG-weighted

gnomAD v4.1

Absent

absent from gnomAD v4.1

Computational evidence

Protein change
AlphaMissense	0.5467	ambiguous · top 7% in DYTN
REVEL	0.41	indeterminate
SaProt	LLR -11.55	damaging
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 4.5	phastCons 1
Regional constraint	o/e 1.05	unconstrained · MANE · 66 kb · p 0.15 · regional, not allelic
Overall
CADD	23.3	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: DYTN
Protein: p.Ser202Pro
Coding: c.604T>C
MANE Select: NM_001093730
dbSNP: rs1699957886
Type: single nucleotide variant
Location: chr2:206699842 (GRCh38)
Gene constraint: LOEUF 1.328 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 69.89

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

Similar variants

DYTN p.Ala112Thr Uncertain significance ★ ⚠ same type
DYTN p.Ala178Val Uncertain significance ★ ⚠ same type
DYTN p.Ala324Val Uncertain significance ★ ⚠ same type
DYTN p.Ala449Ser Uncertain significance ★ ⚠ same type
DYTN p.Ala465Thr Uncertain significance ★ ⚠ same type
DYTN p.Ala52Pro Uncertain significance ★ ⚠ same type
DYTN p.Ala564Thr Uncertain significance ★ ⚠ same type
DYTN p.Ala567Thr 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/dytn-p-ser202pro (accessed [today's date]).

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