Is BAZ2B p.Pro1390Leu (c.4169C>T) pathogenic?

BAZ2B p.Pro1390Leu (c.4169C>T) is classified Uncertain significance in BAZ2B (ClinVar, Single submitter, 1 submitter; last evaluated 2024-01-08). AlphaMissense: likely pathogenic (0.926); Absent from gnomAD v4.1.

How common is BAZ2B p.Pro1390Leu (c.4169C>T) in the general population?

BAZ2B p.Pro1390Leu (c.4169C>T) is absent from gnomAD v4.1 (gnomAD).

What do computational predictors say about BAZ2B p.Pro1390Leu (c.4169C>T)?

AlphaMissense predicts likely pathogenic (score 0.926) — an in-silico prediction, not a clinical call.

BAZ2B p.Pro1390Leu

c.4169C>T · VCV3367599

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely pathogenic

0.926 · 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	0.926	likely pathogenic
REVEL	0.605	indeterminate
SaProt	LLR -8.48	tolerated
⇒ AlphaMissense calls this damaging; SaProt does not; REVEL makes no call.
Splicing
SpliceAI	<0.2	all four deltas below 0.2 · G>C here scores Δ0.32 · evaluated, not missing
Constraint at this position
Conservation	phyloP 12	GERP 1.6, phastCons 1
Regional constraint	o/e 1.01	unconstrained · MANE · 45 kb · p 0.77 · regional, not allelic
Overall
CADD	25.9	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: BAZ2B
Protein: p.Pro1390Leu
Coding: c.4169C>T
MANE Select: NM_013450
Type: single nucleotide variant
Location: chr2:159373089 (GRCh38)
Gene constraint: LOEUF 0.386 · pLI 1.00 · ClinGen HI 1/3 (gnomAD)
Structure: AlphaFold pLDDT 55.23 · 265 PDB

Full BAZ2B gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

BAZ2B p.Met1Thr Pathogenic/Likely pathogenic ★★ same type
BAZ2B p.Arg1290Gln Uncertain significance ★★ ⚠ same type
BAZ2B p.Ile502Val Uncertain significance ★★ ⚠ same type
BAZ2B p.Leu1365Pro Uncertain significance ★★ ⚠ same type
BAZ2B p.Leu587Ser Uncertain significance ★★ ⚠ same type
BAZ2B p.Lys1761Asn Uncertain significance ★★ ⚠ same type
BAZ2B p.Met1013Ile Uncertain significance ★★ ⚠ same type
BAZ2B p.Pro1709Ser 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/baz2b-p-pro1390leu (accessed [today's date]).

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