Is BCOR p.Val797fs (c.2389_2390del) pathogenic?

BCOR p.Val797fs (c.23892390del) is classified Pathogenic/Likely pathogenic in BCOR (ClinVar, Multiple submitters, 3 submitters; last evaluated 2024-03-28). Absent from gnomAD; Associated with BCOR-related disorder.

What condition is associated with BCOR p.Val797fs (c.2389_2390del)?

BCOR p.Val797fs (c.2389_2390del) is associated with BCOR-related disorder, microphthalmia, syndromic 2 (ClinVar).

How common is BCOR p.Val797fs (c.2389_2390del) in the general population?

BCOR p.Val797fs (c.2389_2390del) is absent from gnomAD (gnomAD).

BCOR p.Val797fs

c.2389_2390del · rs2147215369 · VCV1324437

Pathogenic/Likely pathogenic Multiple submitters

Classification

Pathogenic/Likely pathogenic

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 3 submitters

Consequence

frameshift

predicted LoF

gnomAD v4.1

Not reported

no gnomAD frequency available for this variant

Conditions

BCOR-related disorder

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Consequence	frameshift	predicted loss-of-function in a haploinsufficient gene (ClinGen)
NMD	predicted	premature termination codon in exon 4 of 15
Splicing
SpliceAI	—	not assessed · substitutions only
Constraint at this position
Conservation	phyloP -3.1	GERP -3.1

Predicted loss-of-function is descriptive, not an applied PVS1 code.

Population frequency

dbSNP / gnomAD

No gnomAD frequency available for this variant. This is missing data, not an absence: the variant may or may not be present in gnomAD. Rarity (ACMG PM2) and BA1/BS1 cannot be assessed for it.

Variant & gene context

Gene: BCOR
Protein: p.Val797fs
Coding: c.2389_2390del
MANE Select: NM_001123385
dbSNP: rs2147215369
Type: Deletion
Location: chrX:40072956 (GRCh38)
Structure: AlphaFold pLDDT 39.82 · 5 PDB

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

Disease context

BCOR-related disorder

Also linked: microphthalmia, syndromic 2

Similar variants

BCOR p.Val379fs Pathogenic ★★ same condition
BCOR c.2997+1_2997+25del Likely pathogenic ★ same condition
BCOR p.Ala68fs Likely pathogenic ★ same condition
BCOR p.Arg1469fs Pathogenic ★ same condition
BCOR p.Asp1006fs Likely pathogenic ★ same condition
BCOR p.Asp1155fs Pathogenic ★ same condition
BCOR p.Asp1609fs Likely pathogenic ★ same condition
BCOR p.Asp328fs Pathogenic ★ 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-val797fs (accessed [today's date]).

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