Is BAZ1A p.Pro261Ser (c.781C>T) pathogenic?

BAZ1A p.Pro261Ser (c.781C>T) is classified Uncertain significance in BAZ1A (ClinVar, Single submitter, 1 submitter; last evaluated 2025-03-28). AlphaMissense: ambiguous (0.4707); Absent from gnomAD v4.1.

How common is BAZ1A p.Pro261Ser (c.781C>T) in the general population?

BAZ1A p.Pro261Ser (c.781C>T) is absent from gnomAD v4.1 (gnomAD).

What do computational predictors say about BAZ1A p.Pro261Ser (c.781C>T)?

AlphaMissense predicts ambiguous (score 0.4707) — an in-silico prediction, not a clinical call.

BAZ1A p.Pro261Ser

c.781C>T · VCV3989203

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

ambiguous

0.4707 · ACMG-weighted

gnomAD v4.1

Absent

absent from gnomAD v4.1

Computational evidence

Protein change
AlphaMissense	0.4707	ambiguous
REVEL	0.35	indeterminate
SaProt	LLR -6.26	tolerated
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 12	GERP 2.8, phastCons 1
Regional constraint	o/e 0.84	unconstrained · MANE · 74 kb · p 0.0015 · regional, not allelic
Overall
CADD	26.6	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: BAZ1A
Protein: p.Pro261Ser
Coding: c.781C>T
MANE Select: NM_013448
Type: single nucleotide variant
Location: chr14:34802934 (GRCh38)
Gene constraint: LOEUF 0.376 · pLI 1.00 (gnomAD)
Structure: AlphaFold pLDDT 68.97 · 1 PDB

Full BAZ1A gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

BAZ1A p.Arg876Cys Benign ★★ same type
BAZ1A p.Leu1017= Benign ★★ same type
BAZ1A c.1511-1G>T Uncertain significance ★ same type
BAZ1A p.Ala1551Val Uncertain significance ★ ⚠ same type
BAZ1A p.Ala272Val Uncertain significance ★ ⚠ same type
BAZ1A p.Ala298Gly Uncertain significance ★ ⚠ same type
BAZ1A p.Ala304Thr Uncertain significance ★ ⚠ same type
BAZ1A p.Ala337Val 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/baz1a-p-pro261ser (accessed [today's date]).

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