Is BCOR p.Asp1040Val (c.3119A>T) pathogenic?

BCOR p.Asp1040Val (c.3119A>T) is classified Uncertain significance in BCOR (ClinVar, Single submitter, 1 submitter; last evaluated 2022-01-05). AlphaMissense: ambiguous (0.3717); Absent from gnomAD v4.1; Associated with microphthalmia, syndromic 2.

What condition is associated with BCOR p.Asp1040Val (c.3119A>T)?

BCOR p.Asp1040Val (c.3119A>T) is associated with microphthalmia, syndromic 2 (ClinVar).

How common is BCOR p.Asp1040Val (c.3119A>T) in the general population?

BCOR p.Asp1040Val (c.3119A>T) is absent from gnomAD v4.1 (gnomAD).

What do computational predictors say about BCOR p.Asp1040Val (c.3119A>T)?

AlphaMissense predicts ambiguous (score 0.3717) — an in-silico prediction, not a clinical call.

BCOR p.Asp1040Val

c.3119A>T · rs2147175167 · VCV2075259

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

ambiguous

0.3717 · ACMG-weighted

gnomAD v4.1

Absent

absent from gnomAD v4.1

Conditions

microphthalmia, syndromic 2

Computational evidence

Protein change
AlphaMissense	0.3717	ambiguous
REVEL	0.345	indeterminate
SaProt	LLR -6.14	tolerated
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 6.2	GERP 1.7, phastCons 1
Regional constraint	o/e 0.53	unconstrained · MANE · 7,889 bp · p 9.6e-07 · regional, not allelic
Overall
CADD	24.5	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.Asp1040Val
Coding: c.3119A>T
MANE Select: NM_001123385
dbSNP: rs2147175167
Type: single nucleotide variant
Location: chrX:40071092 (GRCh38)
Structure: AlphaFold pLDDT 39.82 · 5 PDB

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

Disease context

microphthalmia, syndromic 2 — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Similar variants

BCOR p.Asp1040= Likely benign 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-asp1040val (accessed [today's date]).

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