Is BCO1 p.Asp52= (c.156C>T) pathogenic?

BCO1 p.Asp52= (c.156C>T) is classified Likely benign in BCO1 (ClinVar, No assertion criteria, 1 submitter; last evaluated 2019-04-11). Ultra-rare (popmax 0.0801%, sas); Associated with BCO1-related disorder.

What condition is associated with BCO1 p.Asp52= (c.156C>T)?

BCO1 p.Asp52= (c.156C>T) is associated with BCO1-related disorder (ClinVar).

How common is BCO1 p.Asp52= (c.156C>T) in the general population?

BCO1 p.Asp52= (c.156C>T) is ultra-rare (popmax 0.0801%, sas) (gnomAD).

BCO1 p.Asp52=

c.156C>T · rs554010904 · VCV3057991

Likely benign No assertion criteria

Classification

Likely benign

ClinVar

Review

No assertion criteria ☆☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

ultra-rare (popmax 0.0801%, sas)

Conditions

BCO1-related disorder

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
REVEL	0.305	indeterminate
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP -4.6	GERP -2.8
Overall
CADD	1.306	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.0801% South Asian · 73/91,088 alleles

Filtering AF 0.0654% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.0599%

Overall 0.013% 210/1,614,238 alleles · ultra-rare exomes 198/1,461,892 · genomes 12/152,346 · joint denominator

Ancestry group	Frequency	1 in
South Asiangrpmax	0.0801%	1,248
Remaining individualsnot grpmax-eligible	0.0144%	6,946
European (non-Finnish)	0.00983%	10,173
Finnishnot grpmax-eligible	0.00937%	10,671
East Asian	0.00668%	14,963
African / African-American	0.004%	25,021

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: BCO1
Protein: p.Asp52=
Coding: c.156C>T
MANE Select: NM_017429
dbSNP: rs554010904
Type: single nucleotide variant
Location: chr16:81245566 (GRCh38)
Gene constraint: LOEUF 1.17 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 90.03

Full BCO1 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

BCO1-related disorder

Similar variants

BCO1 p.Asp52Asn Uncertain significance ★ ⚠ same residue
BCO1 c.1102-10A>G Likely benign same condition
BCO1 p.Ala165= Likely benign same condition
BCO1 p.Ile324Thr Likely benign ⚠ same condition
BCO1 p.Arg266Trp Uncertain significance ★★ ⚠ same type
BCO1 p.Thr170Met Uncertain significance ★★ ⚠ same type
BCO1 c.1101+48C>T Benign ★★ same type
BCO1 c.1102-81T>C Benign ★★ 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/bco1-p-asp52 (accessed [today's date]).

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