Is BCHE p.Asn590= (c.1770C>T) pathogenic?

BCHE p.Asn590= (c.1770C>T) is classified Uncertain significance in BCHE (ClinVar, Single submitter, 1 submitter; last evaluated 2018-01-13). Ultra-rare (popmax 0.0341%, sas); Associated with butyrylcholinesterase deficiency.

What condition is associated with BCHE p.Asn590= (c.1770C>T)?

BCHE p.Asn590= (c.1770C>T) is associated with butyrylcholinesterase deficiency (ClinVar).

How common is BCHE p.Asn590= (c.1770C>T) in the general population?

BCHE p.Asn590= (c.1770C>T) is ultra-rare (popmax 0.0341%, sas) (gnomAD).

How is Hereditary butyrylcholinesterase deficiency inherited?

Typically Autosomal recessive (Orphanet). A genetic counselor can assess individual risk for a family.

BCHE p.Asn590=

c.1770C>T · rs771363401 · VCV344087

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

ultra-rare (popmax 0.0341%, sas)

Conditions

butyrylcholinesterase deficiency

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP -10	GERP -5.5
Overall
CADD	2.242	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.0341% South Asian · 31/90,914 alleles

Filtering AF 0.0247% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.0214%

Overall 0.0102% 165/1,610,370 alleles · ultra-rare

Ancestry group	Frequency	1 in
South Asiangrpmax	0.0341%	2,933
Remaining individualsnot grpmax-eligible	0.0192%	5,195
Admixed American	0.0134%	7,485
East Asian	0.00895%	11,170
European (non-Finnish)	0.00883%	11,320
African / African-American	0.00802%	12,468

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: BCHE
Protein: p.Asn590=
Coding: c.1770C>T
MANE Select: NM_000055
dbSNP: rs771363401
Type: single nucleotide variant
Location: chr3:165773421 (GRCh38)
Gene constraint: LOEUF 1.195 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
Structure: AlphaFold pLDDT 93.30 · 111 PDB

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

Disease context

butyrylcholinesterase deficiency — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

For Hereditary butyrylcholinesterase deficiency (Orphanet):

Inheritance: Autosomal recessive
Onset: Infancy, Neonatal
Prevalence: 1-9 / 100 000 (Europe)

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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/bche-p-asn590 (accessed [today's date]).

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