Is DYNLT2B p.Ser10Ala (c.28T>G) pathogenic?

DYNLT2B p.Ser10Ala (c.28T>G) is classified Uncertain significance in DYNLT2B (ClinVar, Single submitter, 1 submitter; last evaluated 2022-03-18). AlphaMissense: likely benign (0.0595); Very rare (popmax 0.00283%, afr).

How common is DYNLT2B p.Ser10Ala (c.28T>G) in the general population?

DYNLT2B p.Ser10Ala (c.28T>G) is very rare (popmax 0.00283%, afr) (gnomAD).

What do computational predictors say about DYNLT2B p.Ser10Ala (c.28T>G)?

AlphaMissense predicts likely benign (score 0.0595) — an in-silico prediction, not a clinical call.

DYNLT2B p.Ser10Ala

c.28T>G · rs1726941135 · VCV1969060

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.0595 · ACMG-weighted

gnomAD v4.1

Rare

very rare (popmax 0.00283%, afr)

Missense predictors

0/3 damaging

AlphaMissense, REVEL, SaProt

Computational evidence

Protein change
AlphaMissense	0.0595	likely benign
REVEL	0.022	moderately benign-leaning
SaProt	LLR -6.77	tolerated
⇒ AlphaMissense, REVEL and SaProt all call this tolerated.
Splicing
SpliceAI	Δ0.23	donor loss, 2 bp away · masked 0 · deltas
Constraint at this position
Conservation	phyloP -2.5	GERP -1.1
Regional constraint	o/e 0.76	unconstrained · MANE · 27 kb · p 0.0016 · regional, not allelic
Overall
CADD	0.3	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

Grpmax group 0.00283% African / African-American · 2/70,738 alleles

Filtering AF 0.000469% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.000176%

Overall 0.000129% 2/1,553,912 alleles · very rare exomes 0/1,401,848 · genomes 2/152,064 · joint denominator

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: DYNLT2B
Protein: p.Ser10Ala
Coding: c.28T>G
MANE Select: NM_152773
dbSNP: rs1726941135
Type: single nucleotide variant
Location: chr3:196318125 (GRCh38)
Gene constraint: LOEUF 1.236 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 86.89 · 2 PDB
Residue 10: a β-strand

Full DYNLT2B gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

DYNLT2B p.Arg88Ter Pathogenic/Likely pathogenic ★★ same type
DYNLT2B p.Arg110His Uncertain significance ★★ same type
DYNLT2B p.Asn119Ser Uncertain significance ★★ ⚠ same type
DYNLT2B p.Gly6Arg Uncertain significance ★★ ⚠ same type
DYNLT2B p.Gly6Val Uncertain significance ★★ ⚠ same type
DYNLT2B p.Ser4Thr Uncertain significance ★★ ⚠ same type
DYNLT2B p.Val95Leu Uncertain significance ★★ ⚠ same type
DYNLT2B c.113+17C>G Benign ★★ 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/dynlt2b-p-ser10ala (accessed [today's date]).

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