Is DBR1 p.Lys160Arg (c.479A>G) pathogenic?

DBR1 p.Lys160Arg (c.479A>G) is classified Uncertain significance in DBR1 (ClinVar, Multiple submitters, 2 submitters; last evaluated 2024-08-11). AlphaMissense: likely benign (0.0941); Ultra-rare (popmax 0.0338%, afr); Associated with Inborn genetic diseases.

What condition is associated with DBR1 p.Lys160Arg (c.479A>G)?

DBR1 p.Lys160Arg (c.479A>G) is associated with Inborn genetic diseases (ClinVar).

How common is DBR1 p.Lys160Arg (c.479A>G) in the general population?

DBR1 p.Lys160Arg (c.479A>G) is ultra-rare (popmax 0.0338%, afr) (gnomAD).

What do computational predictors say about DBR1 p.Lys160Arg (c.479A>G)?

AlphaMissense predicts likely benign (score 0.0941) — an in-silico prediction, not a clinical call.

DBR1 p.Lys160Arg

c.479A>G · rs139110048 · VCV2076911

Uncertain significance Multiple submitters

Classification

Uncertain significance

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 2 submitters

AlphaMissense

likely benign

0.0941 · ACMG-weighted

gnomAD v4.1

Rare

ultra-rare (popmax 0.0338%, afr)

Missense predictors

0/3 damaging

AlphaMissense, REVEL, SaProt

Conditions

Inborn genetic diseases

Computational evidence

Protein change
AlphaMissense	0.0941	likely benign
REVEL	0.199	benign-leaning
SaProt	LLR -5.55	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 7.8	phastCons 1
Regional constraint	o/e 0.96	unconstrained · MANE · 12 kb · p 0.4 · regional, not allelic
Overall
CADD	21.1	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 0.0338% African / African-American · 25/73,964 alleles

Filtering AF 0.0234% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.02%

Overall 0.00184% 29/1,579,198 alleles · ultra-rare

Ancestry group	Frequency	1 in
African / African-Americangrpmax	0.0338%	2,959
Remaining individualsnot grpmax-eligible	0.00652%	15,343

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: DBR1
Protein: p.Lys160Arg
Coding: c.479A>G
MANE Select: NM_016216
dbSNP: rs139110048
Type: single nucleotide variant
Location: chr3:138170117 (GRCh38)
Gene constraint: LOEUF 0.841 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 79.04

Full DBR1 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

Inborn genetic diseases — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Similar variants

DBR1 p.Lys160Glu Uncertain significance ★ ⚠ same residue
DBR1 p.Ala233Thr Uncertain significance ★★ ⚠ same condition
DBR1 p.Ala443Thr Uncertain significance ★★ ⚠ same condition
DBR1 p.Ala458Asp Uncertain significance ★★ ⚠ same condition
DBR1 p.Arg197Gln Uncertain significance ★★ ⚠ same condition
DBR1 p.Arg527Ser Uncertain significance ★★ ⚠ same condition
DBR1 p.Glu434Asp Uncertain significance ★★ ⚠ same condition
DBR1 p.Gly121Ser Uncertain significance ★★ ⚠ same condition

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/dbr1-p-lys160arg (accessed [today's date]).

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