Is DYNLRB2 p.Glu3Asp (c.9G>C) pathogenic?

DYNLRB2 p.Glu3Asp (c.9G>C) is classified Uncertain significance in DYNLRB2 (ClinVar, Single submitter, 1 submitter; last evaluated 2024-11-15). AlphaMissense: likely benign (0.1233); Very rare (popmax 0.00167%, amr).

How common is DYNLRB2 p.Glu3Asp (c.9G>C) in the general population?

DYNLRB2 p.Glu3Asp (c.9G>C) is very rare (popmax 0.00167%, amr) (gnomAD).

What do computational predictors say about DYNLRB2 p.Glu3Asp (c.9G>C)?

AlphaMissense predicts likely benign (score 0.1233) — an in-silico prediction, not a clinical call.

DYNLRB2 p.Glu3Asp

c.9G>C · VCV3506117

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.1233 · ACMG-weighted

gnomAD v4.1

Rare

very rare (popmax 0.00167%, amr)

Missense predictors

1/3 damaging

AlphaMissense, REVEL, SaProt

Computational evidence

Protein change
AlphaMissense	0.1233	likely benign
REVEL	0.089	moderately benign-leaning
SaProt	LLR -11.53	damaging
⇒ SaProt calls this damaging; AlphaMissense and REVEL do not.
Splicing
SpliceAI	Δ0.24	acceptor gain · deltas
Constraint at this position
Conservation	phyloP 0.88	GERP -0.14, phastCons 1
Regional constraint	o/e 1.21	unconstrained · MANE · 9,478 bp · p 0.025 · regional, not allelic
Overall
CADD	19.03	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 0.00167% Admixed American · 1/60,024 alleles

Filtering AF 0.000763% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.000605%

Overall 0.00116% 17/1,461,674 alleles · very rare

Ancestry group	Frequency	1 in
Admixed Americangrpmax	0.00167%	60,024
Remaining individualsnot grpmax-eligible	0.0016%	62,494
European (non-Finnish)	0.00127%	78,659

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: DYNLRB2
Protein: p.Glu3Asp
Coding: c.9G>C
MANE Select: NM_130897
Type: single nucleotide variant
Location: chr16:80543281 (GRCh38)
Gene constraint: LOEUF 1.624 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 95.08 · 1 PDB

Full DYNLRB2 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

DYNLRB2 p.Leu66= Benign ★★ same type
DYNLRB2 p.Arg10Lys Uncertain significance ★ ⚠ same type
DYNLRB2 p.Arg58Cys Uncertain significance ★ same type
DYNLRB2 p.Arg58His Uncertain significance ★ same type
DYNLRB2 p.Asn36Thr Uncertain significance ★ ⚠ same type
DYNLRB2 p.Asn64Lys Uncertain significance ★ ⚠ same type
DYNLRB2 p.Asn93Ile Uncertain significance ★ ⚠ same type
DYNLRB2 p.Asp83Gly 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/dynlrb2-p-glu3asp (accessed [today's date]).

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