Is BCOR p.Ser1297fs (c.3888_3889del) pathogenic?

BCOR p.Ser1297fs (c.38883889del) is classified Likely pathogenic in BCOR (ClinVar, Single submitter, 1 submitter; last evaluated 2023-02-23). Absent from gnomAD; Associated with microphthalmia, syndromic 2.

What condition is associated with BCOR p.Ser1297fs (c.3888_3889del)?

BCOR p.Ser1297fs (c.3888_3889del) is associated with microphthalmia, syndromic 2 (ClinVar).

How common is BCOR p.Ser1297fs (c.3888_3889del) in the general population?

BCOR p.Ser1297fs (c.3888_3889del) is absent from gnomAD (gnomAD).

BCOR p.Ser1297fs

c.3888_3889del · rs2519607953 · VCV2444306

Likely pathogenic Single submitter

Classification

Likely pathogenic

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

Consequence

frameshift

predicted LoF

gnomAD v4.1

Not reported

no gnomAD frequency available for this variant

Conditions

microphthalmia, syndromic 2

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 9 of 15
Splicing
SpliceAI	—	not assessed · substitutions only
Constraint at this position
Conservation	phyloP 4.4	GERP 1.7, phastCons 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.Ser1297fs
Coding: c.3888_3889del
MANE Select: NM_001123385
dbSNP: rs2519607953
Type: Deletion
Location: chrX:40063030 (GRCh38)
Structure: AlphaFold pLDDT 39.82 · 5 PDB
Residue 1297: the 'disordered' region

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.Val379fs Pathogenic ★★ same condition
BCOR p.Val797fs Pathogenic/Likely pathogenic ★★ same condition
BCOR c.2997+1_2997+25del 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.Asp328fs Pathogenic ★ same condition
BCOR p.Gln1528fs 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-ser1297fs (accessed [today's date]).

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