Is DBX1 p.Ser117Phe (c.350C>T) pathogenic?

DBX1 p.Ser117Phe (c.350C>T) is classified Uncertain significance in DBX1 (ClinVar, Single submitter, 1 submitter; last evaluated 2021-09-27). AlphaMissense: ambiguous (0.427); Very rare (popmax 0.00266%, afr).

How common is DBX1 p.Ser117Phe (c.350C>T) in the general population?

DBX1 p.Ser117Phe (c.350C>T) is very rare (popmax 0.00266%, afr) (gnomAD).

What do computational predictors say about DBX1 p.Ser117Phe (c.350C>T)?

AlphaMissense predicts ambiguous (score 0.427) — an in-silico prediction, not a clinical call.

DBX1 p.Ser117Phe

c.350C>T · rs868480621 · VCV2252101

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

ambiguous

0.427 · ACMG-weighted

gnomAD v4.1

Rare

very rare (popmax 0.00266%, afr)

Computational evidence

Protein change
AlphaMissense	0.427	ambiguous
REVEL	0.554	indeterminate
SaProt	LLR -10.08	damaging
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 12	GERP 1.9, phastCons 1
Regional constraint	o/e 1.08	unconstrained · MANE · 4,107 bp · p 0.095 · regional, not allelic
Overall
CADD	32.0	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 0.00266% African / African-American · 2/75,062 alleles

Filtering AF 0.000442% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.000166%

Overall 0.000137% 2/1,461,670 alleles · very rare

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: DBX1
Protein: p.Ser117Phe
Coding: c.350C>T
MANE Select: NM_001029865
dbSNP: rs868480621
Type: single nucleotide variant
Location: chr11:20159975 (GRCh38)
Gene constraint: LOEUF 0.98 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 63.03

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-ser117phe (accessed [today's date]).

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