Is BOD1 p.Arg151= (c.453A>G) pathogenic?

BOD1 p.Arg151= (c.453A>G) is classified Likely benign in BOD1 (ClinVar, No assertion criteria, 1 submitter; last evaluated 2019-06-21). Rare (popmax 0.429%, afr); Associated with BOD1-related disorder.

What condition is associated with BOD1 p.Arg151= (c.453A>G)?

BOD1 p.Arg151= (c.453A>G) is associated with BOD1-related disorder (ClinVar).

How common is BOD1 p.Arg151= (c.453A>G) in the general population?

BOD1 p.Arg151= (c.453A>G) is rare (popmax 0.429%, afr) (gnomAD).

BOD1 p.Arg151=

c.453A>G · rs150859874 · VCV3043227

Likely benign No assertion criteria

Classification

Likely benign

ClinVar

Review

No assertion criteria ☆☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

rare (popmax 0.429%, afr)

Conditions

BOD1-related disorder

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
REVEL	0.036	moderately benign-leaning
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP -0.045	GERP -1.7, phastCons 0.91
Overall
CADD	10.43	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.429% African / African-American · 317/73,938 alleles

Filtering AF 0.39% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.375%

Overall 0.0233% 376/1,612,960 alleles · rare exomes 223/1,461,252 · genomes 153/151,708 · joint denominator

Ancestry group	Frequency	1 in
African / African-Americangrpmax	0.429%	233
Middle Eastern	0.0825%	1,212
Remaining individualsnot grpmax-eligible	0.0496%	2,014
Admixed American	0.0283%	3,529
South Asian	0.00329%	30,361
European (non-Finnish)	0.000254%	393,342

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: BOD1
Protein: p.Arg151=
Coding: c.453A>G
MANE Select: NM_138369
dbSNP: rs150859874
Type: single nucleotide variant
Location: chr5:173609344 (GRCh38)
Gene constraint: LOEUF 1.335 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 77.06

Full BOD1 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

BOD1-related disorder

Similar variants

BOD1 p.Arg151Ter Likely pathogenic ★ same residue
BOD1 p.Arg151Gln Uncertain significance ★ ⚠ same residue
BOD1 p.Pro172Ala Uncertain significance ★ ⚠ same condition
BOD1 c.*1+6G>A Likely benign same condition
BOD1 p.Ala158= Likely benign same condition
BOD1 p.Asp183= Likely benign same condition
BOD1 p.Lys161= Likely benign same condition
BOD1 p.Ser181= Likely benign 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/bod1-p-arg151 (accessed [today's date]).

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