Is BCOR p.Val1636= (c.4908G>A) pathogenic?

BCOR p.Val1636= (c.4908G>A) is classified Likely benign in BCOR (ClinVar, No assertion criteria, 1 submitter; last evaluated 2021-04-02). Very rare (popmax 0.0035%, afr); Associated with BCOR-related disorder.

What condition is associated with BCOR p.Val1636= (c.4908G>A)?

BCOR p.Val1636= (c.4908G>A) is associated with BCOR-related disorder (ClinVar).

How common is BCOR p.Val1636= (c.4908G>A) in the general population?

BCOR p.Val1636= (c.4908G>A) is very rare (popmax 0.0035%, afr) (gnomAD).

BCOR p.Val1636=

c.4908G>A · rs1198182534 · VCV3030777

Likely benign No assertion criteria

Classification

Likely benign

ClinVar

Review

No assertion criteria ☆☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

very rare (popmax 0.0035%, afr)

Conditions

BCOR-related disorder

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation/SpliceAI carries the signal.
Splicing
SpliceAI	Δ0.26	donor gain · deltas
Pangolin	Δ0.32	gain · loss 0.00 · agrees with SpliceAI · independent
Constraint at this position
Conservation	phyloP 1.4	GERP 0.58, phastCons 1
Overall
CADD	11.83	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.0035% African / African-American · 2/57,104 alleles

Filtering AF 0.000581% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.000217%

Overall 0.00179% 2/111,643 alleles · very rare

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.Val1636=
Coding: c.4908G>A
MANE Select: NM_001123385
dbSNP: rs1198182534
Type: single nucleotide variant
Location: chrX:40053954 (GRCh38)
Structure: AlphaFold pLDDT 39.82 · 5 PDB
Residue 1636: the 'necessary and sufficient for interaction with pcgf1' region

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

Disease context

BCOR-related disorder

Similar variants

BCOR p.Arg1217Ter Pathogenic ★★ same condition
BCOR p.Asp174Asn Uncertain significance ★★ ⚠ same condition
BCOR p.Ile730Leu Uncertain significance ★★ ⚠ same condition
BCOR c.4174-2A>G Likely pathogenic ★ same condition
BCOR p.Glu1052Ter Likely pathogenic ★ same condition
BCOR p.Glu1464Ter Likely pathogenic ★ same condition
BCOR p.Gly86Ter Likely pathogenic ★ same condition
BCOR p.Gln156Pro 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-val1636 (accessed [today's date]).

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