Is BCOR p.Ser1142Gly (c.3424A>G) pathogenic?

BCOR p.Ser1142Gly (c.3424A>G) is classified Likely benign in BCOR (ClinVar, Single submitter, 1 submitter; last evaluated 2024-05-29). AlphaMissense: likely benign (0.0687); Ultra-rare (popmax 0.0211%, sas); Associated with Inborn genetic diseases.

What condition is associated with BCOR p.Ser1142Gly (c.3424A>G)?

BCOR p.Ser1142Gly (c.3424A>G) is associated with Inborn genetic diseases (ClinVar).

How common is BCOR p.Ser1142Gly (c.3424A>G) in the general population?

BCOR p.Ser1142Gly (c.3424A>G) is ultra-rare (popmax 0.0211%, sas) (gnomAD).

What do computational predictors say about BCOR p.Ser1142Gly (c.3424A>G)?

AlphaMissense predicts likely benign (score 0.0687) — an in-silico prediction, not a clinical call.

BCOR p.Ser1142Gly

c.3424A>G · VCV3260715

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.0687 · ACMG-weighted

gnomAD v4.1

Rare

ultra-rare (popmax 0.0211%, sas)

Missense predictors

0/3 damaging

AlphaMissense, REVEL, SaProt

Conditions

Inborn genetic diseases

Computational evidence

Protein change
AlphaMissense	0.0687	likely benign
REVEL	0.097	moderately benign-leaning
SaProt	LLR -7.28	tolerated
⇒ AlphaMissense, REVEL and SaProt all call this tolerated.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 3.4	GERP 1.7, phastCons 1
Regional constraint	o/e 1.07	unconstrained · MANE · 2,355 bp · p 0.26 · regional, not allelic
Overall
CADD	18.3	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 0.0211% South Asian · 12/56,922 alleles

Filtering AF 0.0121% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.00953%

Overall 0.00282% 31/1,098,055 alleles · ultra-rare

Ancestry group	Frequency	1 in
South Asiangrpmax	0.0211%	4,743
Remaining individualsnot grpmax-eligible	0.0021%	47,607
European (non-Finnish)	0.00201%	49,737

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.Ser1142Gly
Coding: c.3424A>G
MANE Select: NM_001123385
Type: single nucleotide variant
Location: chrX:40064414 (GRCh38)
Structure: AlphaFold pLDDT 39.82 · 5 PDB
Residue 1142: the 'disordered' region

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

Disease context

Inborn genetic diseases — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Similar variants

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BCOR p.Ala165Pro Uncertain significance ★★ ⚠ same condition
BCOR p.Arg1231Trp Uncertain significance ★★ ⚠ same condition
BCOR p.Arg763Trp Uncertain significance ★★ ⚠ same condition
BCOR p.Asn193Ser Uncertain significance ★★ ⚠ same condition
BCOR p.Asp1420Asn 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-ser1142gly (accessed [today's date]).

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