Is BAZ1B p.Pro334Leu (c.1001C>T) pathogenic?

BAZ1B p.Pro334Leu (c.1001C>T) is classified Uncertain significance in BAZ1B (ClinVar, Single submitter, 1 submitter; last evaluated 2023-07-14). AlphaMissense: likely benign (0.2172); Absent from gnomAD v4.1.

How common is BAZ1B p.Pro334Leu (c.1001C>T) in the general population?

BAZ1B p.Pro334Leu (c.1001C>T) is absent from gnomAD v4.1 (gnomAD).

What do computational predictors say about BAZ1B p.Pro334Leu (c.1001C>T)?

AlphaMissense predicts likely benign (score 0.2172) — an in-silico prediction, not a clinical call.

BAZ1B p.Pro334Leu

c.1001C>T · rs2484855359 · VCV2612148

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.2172 · ACMG-weighted

gnomAD v4.1

Absent

absent from gnomAD v4.1

Missense predictors

0/3 damaging

AlphaMissense, REVEL, SaProt

Computational evidence

Protein change
AlphaMissense	0.2172	likely benign
REVEL	0.196	benign-leaning
SaProt	LLR -6.82	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 12	GERP 1.7, phastCons 1
Regional constraint	o/e 0.88	unconstrained · MANE · 11 kb · p 0.063 · regional, not allelic
Overall
CADD	25.4	PHRED · no single calibrated threshold — expert panels disagree

ClinVar classifies this uncertain; the computational predictors unanimously lean tolerated — a triage signal, not a reclassification

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: BAZ1B
Protein: p.Pro334Leu
Coding: c.1001C>T
MANE Select: NM_032408
dbSNP: rs2484855359
Type: single nucleotide variant
Location: chr7:73478460 (GRCh38)
Gene constraint: LOEUF 0.201 · pLI 1.00 (gnomAD)
Structure: AlphaFold pLDDT 69.55 · 2 PDB

Full BAZ1B gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

BAZ1B p.Glu720Asp Uncertain significance ★★ ⚠ same type
BAZ1B c.3581-6C>T Likely benign ★★ same type
BAZ1B p.Arg1340Lys Likely benign ★★ same type
BAZ1B p.Gln1434= Benign ★★ same type
BAZ1B p.Glu1142= Benign/Likely benign ★★ same type
BAZ1B p.His939Tyr Benign ★★ same type
BAZ1B p.Pro1448= Benign/Likely benign ★★ same type
BAZ1B p.Ser679= Benign ★★ 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/baz1b-p-pro334leu (accessed [today's date]).

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