Is DBN1 p.Pro384= (c.1152G>A) pathogenic?

DBN1 p.Pro384= (c.1152G>A) is classified Benign in DBN1 (ClinVar, Single submitter, 1 submitter; last evaluated 2018-04-20). Rare (popmax 0.385%, afr).

How common is DBN1 p.Pro384= (c.1152G>A) in the general population?

DBN1 p.Pro384= (c.1152G>A) is rare (popmax 0.385%, afr) (gnomAD).

DBN1 p.Pro384=

c.1152G>A · rs149274225 · VCV782464

Benign Single submitter

Classification

Benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

rare (popmax 0.385%, afr)

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP -4.5	GERP -2.8
Overall
CADD	3.111	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.385% African / African-American · 288/74,800 alleles

Filtering AF 0.348% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.334%

Overall 0.0195% 314/1,610,906 alleles · rare

Ancestry group	Frequency	1 in
African / African-Americangrpmax	0.385%	260
Admixed American	0.0135%	7,418
Remaining individualsnot grpmax-eligible	0.00802%	12,473
South Asian	0.0033%	30,309
Finnishnot grpmax-eligible	0.00158%	63,366
European (non-Finnish)	0.000763%	130,997

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: DBN1
Protein: p.Pro384=
Coding: c.1152G>A
MANE Select: NM_001363541
dbSNP: rs149274225
Type: single nucleotide variant
Location: chr5:177459210 (GRCh38)
Gene constraint: LOEUF 0.347 · pLI 1.00 (gnomAD)
Structure: AlphaFold pLDDT 62.93 · 5 PDB
Residue 384: the 'disordered' region

Full DBN1 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

DBN1 c.86+1283G>A Uncertain significance ★ same type
DBN1 c.86+1286G>A Uncertain significance ★ same type
DBN1 c.86+1299A>T Uncertain significance ★ same type
DBN1 p.Ala126Val Uncertain significance ★ ⚠ same type
DBN1 p.Ala244Val Uncertain significance ★ ⚠ same type
DBN1 p.Ala27Thr Uncertain significance ★ ⚠ same type
DBN1 p.Ala455Val Uncertain significance ★ ⚠ same type
DBN1 p.Ala485Thr 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/dbn1-p-pro384 (accessed [today's date]).

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