Is BCL11B p.Pro319= (c.957C>G) pathogenic?

BCL11B p.Pro319= (c.957C>G) is classified Likely benign in BCL11B (ClinVar, Single submitter, 1 submitter; last evaluated 2022-06-08). Absent from gnomAD v4.1.

How common is BCL11B p.Pro319= (c.957C>G) in the general population?

BCL11B p.Pro319= (c.957C>G) is absent from gnomAD v4.1 (gnomAD).

BCL11B p.Pro319=

c.957C>G · rs763009922 · VCV2183150

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Not reported

no allele count reported in gnomAD v4.1 (AN 1,469,432)

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 -2.2	GERP -3.5
Overall
CADD	6.386	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

No allele count reported in gnomAD v4.1 (AN 1,469,432). 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: BCL11B
Protein: p.Pro319=
Coding: c.957C>G
MANE Select: NM_138576
dbSNP: rs763009922
Type: single nucleotide variant
Location: chr14:99175879 (GRCh38)
Gene constraint: LOEUF 0.462 · pLI 1.00 (gnomAD)
Structure: AlphaFold pLDDT 51.76 · 6 PDB

Full BCL11B gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

BCL11B p.Pro319Ala Uncertain significance ★ ⚠ same residue
BCL11B p.Asn807Lys Pathogenic/Likely pathogenic ★★ ⚠ same type
BCL11B p.Cys808Arg Likely pathogenic ★★ same type
BCL11B p.Tyr824Ter Likely pathogenic ★★ same type
BCL11B p.Ala152Val Uncertain significance ★★ ⚠ same type
BCL11B p.Ala188Thr Uncertain significance ★★ ⚠ same type
BCL11B p.Ala339Val Uncertain significance ★★ ⚠ same type
BCL11B p.Ala424Asp 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/bcl11b-p-pro319 (accessed [today's date]).

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