Is DBX1 p.Ser80Leu (c.239C>T) pathogenic?

DBX1 p.Ser80Leu (c.239C>T) is classified Uncertain significance in DBX1 (ClinVar, Single submitter, 1 submitter; last evaluated 2024-03-07). AlphaMissense: likely benign (0.0811); Absent from gnomAD v4.1.

How common is DBX1 p.Ser80Leu (c.239C>T) in the general population?

DBX1 p.Ser80Leu (c.239C>T) is absent from gnomAD v4.1 (gnomAD).

What do computational predictors say about DBX1 p.Ser80Leu (c.239C>T)?

AlphaMissense predicts likely benign (score 0.0811) — an in-silico prediction, not a clinical call.

DBX1 p.Ser80Leu

c.239C>T · rs1453851303 · VCV3080221

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.0811 · ACMG-weighted

gnomAD v4.1

Absent

absent from gnomAD v4.1

Missense predictors

0/3 damaging

AlphaMissense, REVEL, SaProt

Computational evidence

Protein change
AlphaMissense	0.0811	likely benign
REVEL	0.278	benign-leaning
SaProt	LLR -6.94	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 9.9	GERP 1.9, phastCons 1
Regional constraint	o/e 1.08	unconstrained · MANE · 4,107 bp · p 0.095 · regional, not allelic
Overall
CADD	19.25	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

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: DBX1
Protein: p.Ser80Leu
Coding: c.239C>T
MANE Select: NM_001029865
dbSNP: rs1453851303
Type: single nucleotide variant
Location: chr11:20160086 (GRCh38)
Gene constraint: LOEUF 0.98 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 63.03
Residue 80: the 'disordered' region

Full DBX1 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

DBX1 p.Ala127Pro Uncertain significance ★ ⚠ same type
DBX1 p.Ala127Val Uncertain significance ★ ⚠ same type
DBX1 p.Ala314Thr Uncertain significance ★ ⚠ same type
DBX1 p.Ala314Val Uncertain significance ★ ⚠ same type
DBX1 p.Arg211Leu Uncertain significance ★ ⚠ same type
DBX1 p.Arg237Trp Uncertain significance ★ ⚠ same type
DBX1 p.Arg49Pro Uncertain significance ★ ⚠ same type
DBX1 p.Arg56Ser 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/dbx1-p-ser80leu (accessed [today's date]).

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