Is BCOR p.Ser1603Arg (c.4807A>C) pathogenic?

BCOR p.Ser1603Arg (c.4807A>C) is classified Likely pathogenic in BCOR (ClinVar, No assertion criteria, 1 submitter; last evaluated 2015-12-22). AlphaMissense: likely pathogenic (0.9955); Absent from gnomAD v4.1.

How common is BCOR p.Ser1603Arg (c.4807A>C) in the general population?

BCOR p.Ser1603Arg (c.4807A>C) is absent from gnomAD v4.1 (gnomAD).

What do computational predictors say about BCOR p.Ser1603Arg (c.4807A>C)?

AlphaMissense predicts likely pathogenic (score 0.9955) — an in-silico prediction, not a clinical call.

BCOR p.Ser1603Arg

c.4807A>C · rs1555913327 · VCV545026

Likely pathogenic No assertion criteria

Classification

Likely pathogenic

ClinVar

Review

No assertion criteria ☆☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely pathogenic

0.9955 · ACMG-weighted

gnomAD v4.1

Absent

absent from gnomAD v4.1

Missense predictors

1/2 damaging

AlphaMissense, SaProt · REVEL no call

Computational evidence

Protein change
AlphaMissense	0.9955	likely pathogenic ✓ concordant with ClinVar · top 4% in BCOR
REVEL	0.583	indeterminate
SaProt	LLR -7.50	tolerated
⇒ AlphaMissense calls this damaging; SaProt does not; REVEL makes no call.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 7.8	GERP 1.6, phastCons 1
Regional constraint	o/e 0.91	unconstrained · MANE · 3,308 bp · p 0.29 · regional, not allelic
Overall
CADD	25.0	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.Ser1603Arg
Coding: c.4807A>C
MANE Select: NM_001123385
dbSNP: rs1555913327
Type: single nucleotide variant
Location: chrX:40054268 (GRCh38)
Structure: AlphaFold pLDDT 39.82 · 5 PDB

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

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BCOR p.Arg342Ter Pathogenic ★★ same type
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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-ser1603arg (accessed [today's date]).

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