Is BCOR p.Pro663Leu (c.1988C>T) pathogenic?

BCOR p.Pro663Leu (c.1988C>T) is classified Uncertain significance in BCOR (ClinVar, Single submitter, 1 submitter; last evaluated 2025-07-14). AlphaMissense: likely pathogenic (0.6561); Absent from gnomAD v4.1; Associated with Inborn genetic diseases.

What condition is associated with BCOR p.Pro663Leu (c.1988C>T)?

BCOR p.Pro663Leu (c.1988C>T) is associated with Inborn genetic diseases (ClinVar).

How common is BCOR p.Pro663Leu (c.1988C>T) in the general population?

BCOR p.Pro663Leu (c.1988C>T) is absent from gnomAD v4.1 (gnomAD).

What do computational predictors say about BCOR p.Pro663Leu (c.1988C>T)?

AlphaMissense predicts likely pathogenic (score 0.6561) — an in-silico prediction, not a clinical call.

BCOR p.Pro663Leu

c.1988C>T · VCV4203275

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely pathogenic

0.6561 · ACMG-weighted

gnomAD v4.1

Absent

absent from gnomAD v4.1

Missense predictors

1/2 damaging

AlphaMissense, SaProt · REVEL no call

Conditions

Inborn genetic diseases

Computational evidence

Protein change
AlphaMissense	0.6561	likely pathogenic
REVEL	0.304	indeterminate
SaProt	LLR -6.45	tolerated
⇒ AlphaMissense calls this damaging; SaProt does not; REVEL makes no call.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 10	GERP 1.6, phastCons 1
Regional constraint	o/e 0.90	unconstrained · MANE · 2,116 bp · p 0.013 · regional, not allelic
Overall
CADD	23.1	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.Pro663Leu
Coding: c.1988C>T
MANE Select: NM_001123385
Type: single nucleotide variant
Location: chrX:40073358 (GRCh38)
Structure: AlphaFold pLDDT 39.82 · 5 PDB

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

Disease context

Inborn genetic diseases — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Similar variants

BCOR p.Pro663Thr Uncertain significance ★ ⚠ same residue
BCOR p.Arg810Ter Pathogenic ★★ same condition
BCOR p.Ala1314Asp Uncertain significance ★★ ⚠ same condition
BCOR p.Ala147Thr Uncertain significance ★★ ⚠ same condition
BCOR p.Ala165Pro Uncertain significance ★★ ⚠ same condition
BCOR p.Arg1231Trp Uncertain significance ★★ ⚠ same condition
BCOR p.Arg763Trp Uncertain significance ★★ ⚠ same condition
BCOR p.Asn193Ser 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/bcor-p-pro663leu (accessed [today's date]).

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