Is BCOR p.Glu197Ala (c.590A>C) pathogenic?

BCOR p.Glu197Ala (c.590A>C) is classified Uncertain significance in BCOR (ClinVar, Single submitter, 1 submitter; last evaluated 2022-03-04). AlphaMissense: ambiguous (0.3588); Absent from gnomAD v4.1.

How common is BCOR p.Glu197Ala (c.590A>C) in the general population?

BCOR p.Glu197Ala (c.590A>C) is absent from gnomAD v4.1 (gnomAD).

What do computational predictors say about BCOR p.Glu197Ala (c.590A>C)?

AlphaMissense predicts ambiguous (score 0.3588) — an in-silico prediction, not a clinical call.

BCOR p.Glu197Ala

c.590A>C · rs1216442106 · VCV1704112

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

ambiguous

0.3588 · ACMG-weighted

gnomAD v4.1

Absent

absent from gnomAD v4.1

Missense predictors

0/2 damaging

REVEL, SaProt · AlphaMissense no call

Computational evidence

Protein change
AlphaMissense	0.3588	ambiguous
REVEL	0.274	benign-leaning
SaProt	LLR -4.41	tolerated
⇒ REVEL and SaProt both call this tolerated; AlphaMissense makes no call.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 7.9	GERP 1.6, phastCons 1
Regional constraint	o/e 0.92	unconstrained · MANE · 3,243 bp · p 0.27 · regional, not allelic
Overall
CADD	21.0	PHRED · no single calibrated threshold — expert panels disagree

AlphaMissense carries the ACMG weight for missense; REVEL and SaProt are independent agreement signals.

Population frequency

gnomAD v4.1 · exomes + genomes

Absent from gnomAD v4.1. Not observed in any sequenced alleles — a rarity signal (ACMG PM2-supporting), not evidence of pathogenicity on its own.

Variant & gene context

Gene: BCOR
Protein: p.Glu197Ala
Coding: c.590A>C
MANE Select: NM_001123385
dbSNP: rs1216442106
Type: single nucleotide variant
Location: chrX:40074756 (GRCh38)
Structure: AlphaFold pLDDT 39.82 · 5 PDB

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

Similar variants

BCOR p.Glu197Gly Uncertain significance ⚠ same residue
BCOR p.Glu197fs Likely pathogenic same residue
BCOR p.Arg1163Ter Pathogenic ★★ same type
BCOR p.Arg1164Ter Pathogenic ★★ same type
BCOR p.Arg1217Ter Pathogenic ★★ same type
BCOR p.Arg1514Ter Pathogenic ★★ same type
BCOR p.Arg342Ter Pathogenic ★★ same type
BCOR p.Arg810Ter Pathogenic ★★ 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/bcor-p-glu197ala (accessed [today's date]).

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