Is BOD1 p.Arg151Ter (c.451C>T) pathogenic?

BOD1 p.Arg151Ter (c.451C>T) is classified Likely pathogenic in BOD1 (ClinVar, Single submitter, 1 submitter; last evaluated 2024-11-22). Very rare (popmax 0.00678%, nfe).

How common is BOD1 p.Arg151Ter (c.451C>T) in the general population?

BOD1 p.Arg151Ter (c.451C>T) is very rare (popmax 0.00678%, nfe) (gnomAD).

BOD1 p.Arg151Ter

c.451C>T · VCV3900237

Likely pathogenic Single submitter

Classification

Likely pathogenic

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

Consequence

nonsense (stop-gain)

predicted LoF

gnomAD v4.1

Rare

very rare (popmax 0.00678%, nfe)

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Consequence	nonsense (stop-gain)	predicted loss-of-function
NMD	predicted	premature termination codon in exon 3 of 4
REVEL	0.334	indeterminate
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 4.9	GERP 0.91, phastCons 1
Overall
CADD	39.0	PHRED · no single calibrated threshold — expert panels disagree

Predicted loss-of-function is descriptive, not an applied PVS1 code.

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.00678% European (non-Finnish) · 80/1,180,042 alleles

Filtering AF 0.00554% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.00514%

Overall 0.00551% 89/1,614,094 alleles · very rare exomes 82/1,461,884 · genomes 7/152,210 · joint denominator

Ancestry group	Frequency	1 in
European (non-Finnish)grpmax	0.00678%	14,751
Remaining individualsnot grpmax-eligible	0.0048%	20,829
East Asian	0.00446%	22,446
Admixed American	0.00333%	30,001
African / African-American	0.00267%	37,475

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.Arg151Ter
Coding: c.451C>T
MANE Select: NM_138369
Type: single nucleotide variant
Location: chr5:173609346 (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

Similar variants

BOD1 p.Arg151Gln Uncertain significance ★ ⚠ same residue
BOD1 p.Arg151= Likely benign same residue
BOD1 p.Arg112Ter Pathogenic ★ same type
BOD1 c.238-8C>G Uncertain significance ★ same type
BOD1 p.Ala158Glu Uncertain significance ★ ⚠ same type
BOD1 p.Ala158Val Uncertain significance ★ ⚠ same type
BOD1 p.Ala21Pro Uncertain significance ★ ⚠ same type
BOD1 p.Ala23Thr 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/bod1-p-arg151ter (accessed [today's date]).

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