Is BCOR p.Lys1167Arg (c.3500A>G) pathogenic?

BCOR p.Lys1167Arg (c.3500A>G) is classified Likely benign in BCOR (ClinVar, No assertion criteria, 1 submitter; last evaluated 2019-01-01). AlphaMissense: likely benign (0.1291); Absent from gnomAD v4.1; Associated with intellectual disability.

What condition is associated with BCOR p.Lys1167Arg (c.3500A>G)?

BCOR p.Lys1167Arg (c.3500A>G) is associated with intellectual disability (ClinVar).

How common is BCOR p.Lys1167Arg (c.3500A>G) in the general population?

BCOR p.Lys1167Arg (c.3500A>G) is absent from gnomAD v4.1 (gnomAD).

What do computational predictors say about BCOR p.Lys1167Arg (c.3500A>G)?

AlphaMissense predicts likely benign (score 0.1291) — an in-silico prediction, not a clinical call.

BCOR p.Lys1167Arg

c.3500A>G · rs1935079756 · VCV975186

Likely benign No assertion criteria

Classification

Likely benign

ClinVar

Review

No assertion criteria ☆☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.1291 · ACMG-weighted

gnomAD v4.1

Absent

absent from gnomAD v4.1

Missense predictors

0/3 damaging

AlphaMissense, REVEL, SaProt

Conditions

intellectual disability

Computational evidence

Protein change
AlphaMissense	0.1291	likely benign
REVEL	0.145	moderately benign-leaning
SaProt	LLR -6.14	tolerated
⇒ AlphaMissense, REVEL and SaProt all call this tolerated.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 6.1	GERP 0.73, phastCons 1
Regional constraint	o/e 1.07	unconstrained · MANE · 2,355 bp · p 0.26 · regional, not allelic
Overall
CADD	24.2	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.Lys1167Arg
Coding: c.3500A>G
MANE Select: NM_001123385
dbSNP: rs1935079756
Type: single nucleotide variant
Location: chrX:40064338 (GRCh38)
Structure: AlphaFold pLDDT 39.82 · 5 PDB
Residue 1167: the 'disordered' region

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

Disease context

intellectual disability — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Similar variants

BCOR p.Glu1076Lys Benign/Likely benign ★★ same condition
BCOR c.3847+7G>A Conflicting classifications of pathogenicity ★ same condition
BCOR p.Ala1149Val Conflicting classifications of pathogenicity ★ ⚠ same condition
BCOR p.Gln1074Lys Uncertain significance ★ ⚠ same condition
BCOR p.Leu722Phe Conflicting classifications of pathogenicity ★ ⚠ same condition
BCOR p.Thr819Ser Uncertain significance ★ ⚠ same condition
BCOR p.Ser1551Cys Likely benign ★ ⚠ same condition
BCOR p.Lys1087Asn Likely benign 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-lys1167arg (accessed [today's date]).

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