Is BCL11A p.Pro263= (c.789C>A) pathogenic?

BCL11A p.Pro263= (c.789C>A) is classified Likely benign in BCL11A (ClinVar, No assertion criteria, 1 submitter; last evaluated 2024-06-06). Absent from gnomAD v4.1; Associated with BCL11A-related disorder.

What condition is associated with BCL11A p.Pro263= (c.789C>A)?

BCL11A p.Pro263= (c.789C>A) is associated with BCL11A-related disorder (ClinVar).

How common is BCL11A p.Pro263= (c.789C>A) in the general population?

BCL11A p.Pro263= (c.789C>A) is absent from gnomAD v4.1 (gnomAD).

BCL11A p.Pro263=

c.789C>A · VCV3344768

Likely benign No assertion criteria

Classification

Likely benign

ClinVar

Review

No assertion criteria ☆☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Absent

absent from gnomAD v4.1

Conditions

BCL11A-related disorder

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 12	GERP 2.7, phastCons 1
Overall
CADD	13.55	PHRED · no single calibrated threshold — expert panels disagree

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: BCL11A
Protein: p.Pro263=
Coding: c.789C>A
MANE Select: NM_022893
Type: single nucleotide variant
Location: chr2:60462123 (GRCh38)
Gene constraint: LOEUF 0.125 · pLI 1.00 · ClinGen HI 3/3 (gnomAD)
Structure: AlphaFold pLDDT 53.09 · 17 PDB

Full BCL11A gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

BCL11A-related disorder

Similar variants

BCL11A p.Pro263Thr Uncertain significance ★ same residue
BCL11A c.385+2T>G Likely pathogenic ★ same condition
BCL11A c.488-2A>G Likely pathogenic ★ same condition
BCL11A p.Glu526Ter Likely pathogenic ★ same condition
BCL11A p.Ile90Met Likely pathogenic ★ ⚠ same condition
BCL11A p.Arg196Ser Uncertain significance ★ ⚠ same condition
BCL11A p.Met339Val Uncertain significance ★ ⚠ same condition
BCL11A c.488-1G>C Likely 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/bcl11a-p-pro263 (accessed [today's date]).

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