Is DYNC2I2 p.Pro402Ser (c.1204C>T) pathogenic?

DYNC2I2 p.Pro402Ser (c.1204C>T) is classified Uncertain significance in DYNC2I2 (ClinVar, Single submitter, 1 submitter; last evaluated 2019-08-22). AlphaMissense: likely benign (0.3146); Very rare (popmax 8.65e-05%, nfe).

How common is DYNC2I2 p.Pro402Ser (c.1204C>T) in the general population?

DYNC2I2 p.Pro402Ser (c.1204C>T) is very rare (popmax 8.65e-05%, nfe) (gnomAD).

What do computational predictors say about DYNC2I2 p.Pro402Ser (c.1204C>T)?

AlphaMissense predicts likely benign (score 0.3146) — an in-silico prediction, not a clinical call.

DYNC2I2 p.Pro402Ser

c.1204C>T · VCV4904842

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.3146 · ACMG-weighted

gnomAD v4.1

Rare

very rare (popmax 8.65e-05%, nfe)

Missense predictors

2/3 damaging

AlphaMissense, REVEL, SaProt

Computational evidence

Protein change
AlphaMissense	0.3146	likely benign
REVEL	0.742	pathogenic-leaning
SaProt	LLR -11.78	damaging
⇒ REVEL and SaProt call this damaging; AlphaMissense does not.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 12	GERP 1.5, phastCons 1
Regional constraint	o/e 1.02	unconstrained · MANE · 23 kb · p 0.59 · regional, not allelic
Overall
CADD	29.0	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

Grpmax group 8.65e-05% European (non-Finnish) · 1/1,156,380 alleles

Overall 7.06e-05% 1/1,416,288 alleles · very rare

Rarity supports pathogenicity (ACMG PM2); frequency above a disease-specific BA1/BS1 threshold argues against it. A variant frequent in one ancestry group can be near-absent in others, so a single global figure can mislead.

Variant & gene context

Gene: DYNC2I2
Protein: p.Pro402Ser
Coding: c.1204C>T
MANE Select: NM_052844
Type: single nucleotide variant
Location: chr9:128634699 (GRCh38)
Gene constraint: LOEUF 1.036 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 82.66 · 4 PDB

Full DYNC2I2 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

DYNC2I2 c.1372+1G>A Pathogenic/Likely pathogenic ★★ same type
DYNC2I2 p.Arg121Ter Pathogenic ★★ same type
DYNC2I2 p.Arg182Trp Pathogenic/Likely pathogenic ★★ ⚠ same type
DYNC2I2 p.Arg447Trp Pathogenic/Likely pathogenic ★★ same type
DYNC2I2 p.Ala131Val Uncertain significance ★★ ⚠ same type
DYNC2I2 p.Ala13Gly Uncertain significance ★★ ⚠ same type
DYNC2I2 p.Ala219Thr Uncertain significance ★★ ⚠ same type
DYNC2I2 p.Ala369Val 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/dync2i2-p-pro402ser (accessed [today's date]).

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