Is DCTN1 p.Ala810Val (c.2429C>T) pathogenic?

DCTN1 p.Ala810Val (c.2429C>T) is classified Uncertain significance in DCTN1 (ClinVar, Single submitter, 1 submitter; last evaluated 2022-03-10). AlphaMissense: likely benign (0.068); Very rare (popmax 0.0011%, sas).

How common is DCTN1 p.Ala810Val (c.2429C>T) in the general population?

DCTN1 p.Ala810Val (c.2429C>T) is very rare (popmax 0.0011%, sas) (gnomAD).

What do computational predictors say about DCTN1 p.Ala810Val (c.2429C>T)?

AlphaMissense predicts likely benign (score 0.068) — an in-silico prediction, not a clinical call.

DCTN1 p.Ala810Val

c.2429C>T · rs372500630 · VCV2440720

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.068 · ACMG-weighted

gnomAD v4.1

Rare

very rare (popmax 0.0011%, sas)

Missense predictors

0/3 damaging

AlphaMissense, REVEL, SaProt

Computational evidence

Protein change
AlphaMissense	0.068	likely benign
REVEL	0.257	benign-leaning
SaProt	LLR -5.03	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 12	GERP 2.3, phastCons 1
Regional constraint	o/e 0.97	unconstrained · MANE · 3,200 bp · p 0.5 · regional, not allelic
Overall
CADD	23.5	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 0.0011% South Asian · 1/91,086 alleles

Overall 0.000137% 2/1,461,892 alleles · very rare

Ancestry group	Frequency	1 in
South Asiangrpmax	0.0011%	91,086
European (non-Finnish)	8.47e-05%	1,180,048

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: DCTN1
Protein: p.Ala810Val
Coding: c.2429C>T
MANE Select: NM_004082
dbSNP: rs372500630
Type: single nucleotide variant
Location: chr2:74366820 (GRCh38)
Gene constraint: LOEUF 0.448 · pLI 1.00 (gnomAD)
Structure: AlphaFold pLDDT 77.43 · 13 PDB

Full DCTN1 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

DCTN1 p.Ala810Gly Uncertain significance ★ ⚠ same residue
DCTN1 p.Ala810= Likely benign ★ same residue
DCTN1 c.279+1G>T Pathogenic/Likely pathogenic ★★ same type
DCTN1 p.Gln93His Pathogenic/Likely pathogenic ★★ same type
DCTN1 p.Gly71Glu Pathogenic ★★ same type
DCTN1 p.Tyr78His Likely pathogenic ★★ same type
DCTN1 c.1128-3C>G Uncertain significance ★★ same type
DCTN1 c.1288-10C>G 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/dctn1-p-ala810val (accessed [today's date]).

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