Is BCOR p.Arg1209His (c.3626G>A) pathogenic?

BCOR p.Arg1209His (c.3626G>A) is classified Uncertain significance in BCOR (ClinVar, Single submitter, 1 submitter; last evaluated 2019-05-30). AlphaMissense: likely pathogenic (0.6304); Very rare (popmax 0.00296%, eas).

How common is BCOR p.Arg1209His (c.3626G>A) in the general population?

BCOR p.Arg1209His (c.3626G>A) is very rare (popmax 0.00296%, eas) (gnomAD).

What do computational predictors say about BCOR p.Arg1209His (c.3626G>A)?

AlphaMissense predicts likely pathogenic (score 0.6304) — an in-silico prediction, not a clinical call.

BCOR p.Arg1209His

c.3626G>A · rs1422527923 · VCV1305987

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely pathogenic

0.6304 · ACMG-weighted

gnomAD v4.1

Rare

very rare (popmax 0.00296%, eas)

Missense predictors

1/3 damaging

AlphaMissense, REVEL, SaProt

Computational evidence

Protein change
AlphaMissense	0.6304	likely pathogenic
REVEL	0.247	benign-leaning
SaProt	LLR -7.75	tolerated
⇒ AlphaMissense calls this damaging; REVEL and SaProt do not.
Splicing
SpliceAI	<0.2	all four deltas below 0.2 · C>G here scores Δ0.37 · evaluated, not missing
Constraint at this position
Conservation	phyloP 4	GERP 1.7, phastCons 1
Regional constraint	o/e 1.07	unconstrained · MANE · 2,355 bp · p 0.26 · regional, not allelic
Overall
CADD	25.3	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 0.00296% East Asian · 1/33,831 alleles

Filtering AF 0.000164% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.000119%

Overall 0.000637% 7/1,098,234 alleles · very rare

Ancestry group	Frequency	1 in
East Asiangrpmax	0.00296%	33,831
South Asian	0.00175%	56,996
European (non-Finnish)	0.000558%	179,094

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.Arg1209His
Coding: c.3626G>A
MANE Select: NM_001123385
dbSNP: rs1422527923
Type: single nucleotide variant
Location: chrX:40063829 (GRCh38)
Structure: AlphaFold pLDDT 39.82 · 5 PDB

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

Similar variants

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BCOR p.Arg342Ter Pathogenic ★★ same type
BCOR p.Arg810Ter Pathogenic ★★ same type
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BCOR p.Ala1262Ser Uncertain significance ★★ ⚠ same type

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-arg1209his (accessed [today's date]).

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