Is DYNC2I2 p.Ser399Thr (c.1196G>C) pathogenic?

DYNC2I2 p.Ser399Thr (c.1196G>C) is classified Uncertain significance in DYNC2I2 (ClinVar, Single submitter, 1 submitter; last evaluated 2025-12-09). AlphaMissense: likely benign (0.1401); Absent from gnomAD v4.1; Associated with Inborn genetic diseases.

What condition is associated with DYNC2I2 p.Ser399Thr (c.1196G>C)?

DYNC2I2 p.Ser399Thr (c.1196G>C) is associated with Inborn genetic diseases (ClinVar).

How common is DYNC2I2 p.Ser399Thr (c.1196G>C) in the general population?

DYNC2I2 p.Ser399Thr (c.1196G>C) is absent from gnomAD v4.1 (gnomAD).

What do computational predictors say about DYNC2I2 p.Ser399Thr (c.1196G>C)?

AlphaMissense predicts likely benign (score 0.1401) — an in-silico prediction, not a clinical call.

DYNC2I2 p.Ser399Thr

c.1196G>C · VCV4618168

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.1401 · ACMG-weighted

gnomAD v4.1

Absent

absent from gnomAD v4.1

Missense predictors

0/3 damaging

AlphaMissense, REVEL, SaProt

Conditions

Inborn genetic diseases

Computational evidence

Protein change
AlphaMissense	0.1401	likely benign
REVEL	0.061	moderately benign-leaning
SaProt	LLR -9.80	tolerated
⇒ AlphaMissense, REVEL and SaProt all call this tolerated.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 4.8	GERP 0.45, phastCons 1
Regional constraint	o/e 1.02	unconstrained · MANE · 23 kb · p 0.59 · regional, not allelic
Overall
CADD	22.9	PHRED · no single calibrated threshold — expert panels disagree

ClinVar classifies this uncertain; the computational predictors unanimously lean tolerated — a triage signal, not a reclassification

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: DYNC2I2
Protein: p.Ser399Thr
Coding: c.1196G>C
MANE Select: NM_052844
Type: single nucleotide variant
Location: chr9:128634707 (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

Disease context

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

Similar variants

DYNC2I2 p.Ser399Asn Uncertain significance ★ ⚠ same residue
DYNC2I2 p.Ala13Gly Uncertain significance ★★ ⚠ same condition
DYNC2I2 p.Ala369Val Uncertain significance ★★ ⚠ same condition
DYNC2I2 p.Ala5Gly Uncertain significance ★★ ⚠ same condition
DYNC2I2 p.Arg113Gln Uncertain significance ★★ ⚠ same condition
DYNC2I2 p.Arg202Gln Uncertain significance ★★ ⚠ same condition
DYNC2I2 p.Arg249His Uncertain significance ★★ ⚠ same condition
DYNC2I2 p.Arg257Cys 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/dync2i2-p-ser399thr (accessed [today's date]).

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