Is BOD1 p.Asp183= (c.549C>T) pathogenic?

BOD1 p.Asp183= (c.549C>T) is classified Likely benign in BOD1 (ClinVar, No assertion criteria, 1 submitter; last evaluated 2019-05-15). Ultra-rare (popmax 0.0439%, sas); Associated with BOD1-related disorder.

What condition is associated with BOD1 p.Asp183= (c.549C>T)?

BOD1 p.Asp183= (c.549C>T) is associated with BOD1-related disorder (ClinVar).

How common is BOD1 p.Asp183= (c.549C>T) in the general population?

BOD1 p.Asp183= (c.549C>T) is ultra-rare (popmax 0.0439%, sas) (gnomAD).

BOD1 p.Asp183=

c.549C>T · rs751399216 · VCV3042301

Likely benign No assertion criteria

Classification

Likely benign

ClinVar

Review

No assertion criteria ☆☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

ultra-rare (popmax 0.0439%, sas)

Conditions

BOD1-related disorder

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
REVEL	0.091	moderately benign-leaning
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP -3.3	GERP -3.4
Overall
CADD	0.234	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.0439% South Asian · 40/91,028 alleles

Filtering AF 0.0331% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.0293%

Overall 0.00248% 40/1,613,660 alleles · ultra-rare exomes 37/1,461,412 · genomes 3/152,248 · joint denominator

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.Asp183=
Coding: c.549C>T
MANE Select: NM_138369
dbSNP: rs751399216
Type: single nucleotide variant
Location: chr5:173609248 (GRCh38)
Gene constraint: LOEUF 1.335 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 77.06
Residue 183: the 'disordered' region

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

Disease context

BOD1-related disorder

Similar variants

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.Arg151= Likely benign same condition
BOD1 p.Lys161= Likely benign same condition
BOD1 p.Ser181= Likely benign same condition
BOD1 p.Ile153fs Uncertain significance same condition
BOD1 p.Ter186LysextTer? 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-asp183 (accessed [today's date]).

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