Is BCOR p.Ser1551Cys (c.4652C>G) pathogenic?

BCOR p.Ser1551Cys (c.4652C>G) is classified Likely benign in BCOR (ClinVar, Single submitter, 1 submitter; last evaluated 2020-03-27). AlphaMissense: ambiguous (0.5388); Very rare (popmax 0.00838%, nfe); Associated with intellectual disability.

What condition is associated with BCOR p.Ser1551Cys (c.4652C>G)?

BCOR p.Ser1551Cys (c.4652C>G) is associated with intellectual disability (ClinVar).

How common is BCOR p.Ser1551Cys (c.4652C>G) in the general population?

BCOR p.Ser1551Cys (c.4652C>G) is very rare (popmax 0.00838%, nfe) (gnomAD).

What do computational predictors say about BCOR p.Ser1551Cys (c.4652C>G)?

AlphaMissense predicts ambiguous (score 0.5388) — an in-silico prediction, not a clinical call.

BCOR p.Ser1551Cys

c.4652C>G · VCV4074799

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

ambiguous

0.5388 · ACMG-weighted

gnomAD v4.1

Rare

very rare (popmax 0.00838%, nfe)

Missense predictors

1/2 damaging

REVEL, SaProt · AlphaMissense no call

Conditions

intellectual disability

Computational evidence

Protein change
AlphaMissense	0.5388	ambiguous
REVEL	0.674	pathogenic-leaning
SaProt	LLR -7.53	tolerated
⇒ REVEL calls this damaging; SaProt does not; AlphaMissense makes no call.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 9.9	GERP 1.7, phastCons 1
Regional constraint	o/e 0.46	unconstrained · MANE · 6,813 bp · p 5e-08 · regional, not allelic
Overall
CADD	24.7	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

Grpmax group 0.00838% European (non-Finnish) · 75/895,071 alleles

Filtering AF 0.00684% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.00624%

Overall 0.00702% 77/1,097,640 alleles · very rare

Ancestry group	Frequency	1 in
European (non-Finnish)grpmax	0.00838%	11,934
Remaining individualsnot grpmax-eligible	0.0042%	23,821

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: BCOR
Protein: p.Ser1551Cys
Coding: c.4652C>G
MANE Select: NM_001123385
Type: single nucleotide variant
Location: chrX:40055457 (GRCh38)
Structure: AlphaFold pLDDT 39.82 · 5 PDB

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.Lys1087Asn Likely benign same condition
BCOR p.Lys1167Arg 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-ser1551cys (accessed [today's date]).

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