Is BCOR p.Val1102Gly (c.3305T>G) pathogenic?

BCOR p.Val1102Gly (c.3305T>G) is classified Benign/Likely benign in BCOR (ClinVar, Multiple submitters, 4 submitters; last evaluated 2025-10-02). AlphaMissense: likely benign (0.0951); Rare (popmax 0.162%, afr); Associated with History of neurodevelopmental disorder.

What condition is associated with BCOR p.Val1102Gly (c.3305T>G)?

BCOR p.Val1102Gly (c.3305T>G) is associated with History of neurodevelopmental disorder, microphthalmia, syndromic 2 (ClinVar).

How common is BCOR p.Val1102Gly (c.3305T>G) in the general population?

BCOR p.Val1102Gly (c.3305T>G) is rare (popmax 0.162%, afr) (gnomAD).

What do computational predictors say about BCOR p.Val1102Gly (c.3305T>G)?

AlphaMissense predicts likely benign (score 0.0951) — an in-silico prediction, not a clinical call.

BCOR p.Val1102Gly

c.3305T>G · rs111622737 · VCV590251

Benign/Likely benign Multiple submitters

Classification

Benign/Likely benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 4 submitters

AlphaMissense

likely benign

0.0951 · ACMG-weighted

gnomAD v4.1

Rare

rare (popmax 0.162%, afr)

Missense predictors

0/3 damaging

AlphaMissense, REVEL, SaProt

Conditions

History of neurodevelopmental disorder

Computational evidence

Protein change
AlphaMissense	0.0951	likely benign
REVEL	0.235	benign-leaning
SaProt	LLR -6.52	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 1.8	GERP -1.8, phastCons 0.33
Regional constraint	o/e 1.07	unconstrained · MANE · 2,355 bp · p 0.26 · regional, not allelic
Overall
CADD	6.846	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 0.162% African / African-American · 93/57,342 alleles

Filtering AF 0.135% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.126%

Overall 0.0139% 168/1,210,386 alleles · rare

Ancestry group	Frequency	1 in
African / African-Americangrpmax	0.162%	617
Remaining individualsnot grpmax-eligible	0.13%	768
Admixed American	0.0283%	3,534

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.Val1102Gly
Coding: c.3305T>G
MANE Select: NM_001123385
dbSNP: rs111622737
Type: single nucleotide variant
Location: chrX:40064533 (GRCh38)
Structure: AlphaFold pLDDT 39.82 · 5 PDB
Residue 1102: the 'disordered' region

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

Disease context

History of neurodevelopmental disorder — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Also linked: microphthalmia, syndromic 2

Similar variants

BCOR p.Val1102Ala Conflicting classifications of pathogenicity ★ ⚠ same residue
BCOR p.Arg1163Ter Pathogenic ★★ same condition
BCOR p.Arg1217Ter Pathogenic ★★ same condition
BCOR p.Arg1514Ter Pathogenic ★★ same condition
BCOR p.Arg342Ter Pathogenic ★★ same condition
BCOR p.Arg976Ter Pathogenic ★★ same condition
BCOR p.Ala1262Ser Uncertain significance ★★ ⚠ same condition
BCOR p.Ala1307Pro 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-val1102gly (accessed [today's date]).

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