Is BOD1 p.Ser181= (c.543T>C) pathogenic?

BOD1 p.Ser181= (c.543T>C) is classified Likely benign in BOD1 (ClinVar, No assertion criteria, 1 submitter; last evaluated 2019-10-17). Low-frequency (popmax 2.05%, afr); Associated with BOD1-related disorder.

What condition is associated with BOD1 p.Ser181= (c.543T>C)?

BOD1 p.Ser181= (c.543T>C) is associated with BOD1-related disorder (ClinVar).

How common is BOD1 p.Ser181= (c.543T>C) in the general population?

BOD1 p.Ser181= (c.543T>C) is low-frequency (popmax 2.05%, afr) (gnomAD).

BOD1 p.Ser181=

c.543T>C · rs77014290 · VCV3056759

Likely benign No assertion criteria

Classification

Likely benign

ClinVar

Review

No assertion criteria ☆☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

low-frequency (popmax 2.05%, afr)

Conditions

BOD1-related disorder

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
REVEL	0.129	moderately benign-leaning
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 0.46	GERP -0.19, phastCons 0.98
Overall
CADD	9.996	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 2.05% African / African-American · 1,147/55,896 alleles

Filtering AF 1.95% ClinGen BA1/BS1 input FAF95, joint · FAF99 1.91%

Overall 0.886% 11,720/1,323,096 alleles · low-frequency exomes 11,577/1,179,692 · genomes 143/143,404 · joint denominator

Ancestry group	Frequency	1 in
African / African-Americangrpmax	2.05%	49
Middle Eastern	1.19%	84
Ashkenazi Jewishnot grpmax-eligible	1.02%	98
Admixed American	0.965%	104
Remaining individualsnot grpmax-eligible	0.917%	109
European (non-Finnish)	0.884%	113
South Asian	0.74%	135
Finnishnot grpmax-eligible	0.454%	220
East Asian	0.0156%	6,403

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.Ser181=
Coding: c.543T>C
MANE Select: NM_138369
dbSNP: rs77014290
Type: single nucleotide variant
Location: chr5:173609254 (GRCh38)
Gene constraint: LOEUF 1.335 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 77.06
Residue 181: 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.Ser181Thr 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.Arg151= Likely benign same condition
BOD1 p.Asp183= Likely benign same condition
BOD1 p.Lys161= Likely benign same condition
BOD1 p.Ile153fs 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/bod1-p-ser181 (accessed [today's date]).

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