Is DCTN2 p.Ala7Ser (c.19G>T) pathogenic?

DCTN2 p.Ala7Ser (c.19G>T) is classified Uncertain significance in DCTN2 (ClinVar, Single submitter, 1 submitter; last evaluated 2021-07-01). AlphaMissense: ambiguous (0.5212); Absent from gnomAD v4.1.

How common is DCTN2 p.Ala7Ser (c.19G>T) in the general population?

DCTN2 p.Ala7Ser (c.19G>T) is absent from gnomAD v4.1 (gnomAD).

What do computational predictors say about DCTN2 p.Ala7Ser (c.19G>T)?

AlphaMissense predicts ambiguous (score 0.5212) — an in-silico prediction, not a clinical call.

DCTN2 p.Ala7Ser

c.19G>T · rs868277886 · VCV1298549

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

ambiguous

0.5212 · ACMG-weighted

gnomAD v4.1

Not reported

no allele count reported in gnomAD v4.1 (AN 1,285,180)

Missense predictors

0/2 damaging

REVEL, SaProt · AlphaMissense no call

Computational evidence

Protein change
AlphaMissense	0.5212	ambiguous
REVEL	0.111	moderately benign-leaning
SaProt	LLR -7.75	tolerated
⇒ REVEL and SaProt both call this tolerated; AlphaMissense makes no call.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 7.6	GERP 1, phastCons 1
Regional constraint	o/e 0.62	unconstrained · MANE · 13 kb · p 2.4e-07 · regional, not allelic
Overall
CADD	25.9	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

No allele count reported in gnomAD v4.1 (AN 1,285,180). This is missing data, not an absence: the variant may or may not be present in gnomAD. Rarity (ACMG PM2) and BA1/BS1 cannot be assessed for it.

Variant & gene context

Gene: DCTN2
Protein: p.Ala7Ser
Coding: c.19G>T
MANE Select: NM_001261413
dbSNP: rs868277886
Type: single nucleotide variant
Location: chr12:57547045 (GRCh38)
Gene constraint: LOEUF 0.54 · pLI 0.87 (gnomAD)
Structure: AlphaFold pLDDT 77.22 · 2 PDB
Residue 7: an α-helix; the 'disordered' region

Full DCTN2 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

DCTN2 c.1119+7G>A Uncertain significance ★ same type
DCTN2 p.Ala162Gly Uncertain significance ★ ⚠ same type
DCTN2 p.Arg332Ile Uncertain significance ★ ⚠ same type
DCTN2 p.Arg379Cys Conflicting classifications of pathogenicity ★ ⚠ same type
DCTN2 p.Arg395Gln Uncertain significance ★ ⚠ same type
DCTN2 p.Asp168Val Uncertain significance ★ ⚠ same type
DCTN2 p.Asp216Asn Uncertain significance ★ ⚠ same type
DCTN2 p.Asp216Glu 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/dctn2-p-ala7ser (accessed [today's date]).

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