Is DYNC1H1 p.Ser3111Arg (c.9333T>A) pathogenic?

DYNC1H1 p.Ser3111Arg (c.9333T>A) is classified Uncertain significance in DYNC1H1 (ClinVar, Single submitter, 1 submitter; last evaluated 2016-03-15). AlphaMissense: likely pathogenic (0.615); Absent from gnomAD v4.1.

How common is DYNC1H1 p.Ser3111Arg (c.9333T>A) in the general population?

DYNC1H1 p.Ser3111Arg (c.9333T>A) is absent from gnomAD v4.1 (gnomAD).

What do computational predictors say about DYNC1H1 p.Ser3111Arg (c.9333T>A)?

AlphaMissense predicts likely pathogenic (score 0.615) — an in-silico prediction, not a clinical call.

DYNC1H1 p.Ser3111Arg

c.9333T>A · rs879254260 · VCV246442

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely pathogenic

0.615 · ACMG-weighted

gnomAD v4.1

Absent

absent from gnomAD v4.1

Missense predictors

1/2 damaging

AlphaMissense, REVEL

Computational evidence

Protein change
AlphaMissense	0.615	likely pathogenic
REVEL	0.179	moderately benign-leaning
⇒ AlphaMissense calls this damaging; REVEL does not.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP -1.9	GERP -4.9
Regional constraint	o/e 0.52	unconstrained · MANE · 1,681 bp · p 6.4e-08 · regional, not allelic
Overall
CADD	13.74	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: DYNC1H1
Protein: p.Ser3111Arg
Coding: c.9333T>A
MANE Select: NM_001376
dbSNP: rs879254260
Type: single nucleotide variant
Location: chr14:102028006 (GRCh38)
Gene constraint: LOEUF 0.117 · pLI 1.00 · ClinGen HI 0/3 (gnomAD)
Residue 3111: a β-strand; the 'aaa 4' region

Full DYNC1H1 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

DYNC1H1 p.Ser3111Gly Uncertain significance ★★ same residue
DYNC1H1 p.Ser3111Thr Likely benign ★ same residue
DYNC1H1 c.4396-1G>C Likely pathogenic ★★ same type
DYNC1H1 p.Ala4519Val Likely pathogenic ★★ same type
DYNC1H1 p.Arg1567Gln Pathogenic/Likely pathogenic ★★ same type
DYNC1H1 p.Arg1623Gln Pathogenic/Likely pathogenic ★★ same type
DYNC1H1 p.Arg1623Trp Pathogenic ★★ same type
DYNC1H1 p.Arg1962Cys Pathogenic ★★ 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/dync1h1-p-ser3111arg (accessed [today's date]).

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