Is BAZ1B p.Pro1320Ser (c.3958C>T) pathogenic?

BAZ1B p.Pro1320Ser (c.3958C>T) is classified Uncertain significance in BAZ1B (ClinVar, Single submitter, 1 submitter; last evaluated 2024-06-02). AlphaMissense: likely benign (0.0729); Very rare (popmax 0.00237%, nfe).

How common is BAZ1B p.Pro1320Ser (c.3958C>T) in the general population?

BAZ1B p.Pro1320Ser (c.3958C>T) is very rare (popmax 0.00237%, nfe) (gnomAD).

What do computational predictors say about BAZ1B p.Pro1320Ser (c.3958C>T)?

AlphaMissense predicts likely benign (score 0.0729) — an in-silico prediction, not a clinical call.

BAZ1B p.Pro1320Ser

c.3958C>T · VCV3260478

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.0729 · ACMG-weighted

gnomAD v4.1

Rare

very rare (popmax 0.00237%, nfe)

Missense predictors

0/3 damaging

AlphaMissense, REVEL, SaProt

Computational evidence

Protein change
AlphaMissense	0.0729	likely benign
REVEL	0.033	moderately benign-leaning
SaProt	LLR -5.95	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 0.58	GERP -3.4, phastCons 0.052
Regional constraint	o/e 0.80	unconstrained · MANE · 7,402 bp · p 0.00031 · regional, not allelic
Overall
CADD	7.344	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

Grpmax group 0.00237% European (non-Finnish) · 28/1,179,906 alleles

Filtering AF 0.00165% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.00142%

Overall 0.00186% 30/1,613,856 alleles · very rare exomes 30/1,461,536 · genomes 0/152,320 · joint denominator

Ancestry group	Frequency	1 in
European (non-Finnish)grpmax	0.00237%	42,140
East Asian	0.00223%	44,858
Remaining individualsnot grpmax-eligible	0.0016%	62,496

Rarity supports pathogenicity (ACMG PM2); frequency above a disease-specific BA1/BS1 threshold argues against it. A variant frequent in one ancestry group can be near-absent in others, so a single global figure can mislead.

Variant & gene context

Gene: BAZ1B
Protein: p.Pro1320Ser
Coding: c.3958C>T
MANE Select: NM_032408
Type: single nucleotide variant
Location: chr7:73444016 (GRCh38)
Gene constraint: LOEUF 0.201 · pLI 1.00 (gnomAD)
Structure: AlphaFold pLDDT 69.55 · 2 PDB
Residue 1320: the 'disordered' region

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-pro1320ser (accessed [today's date]).

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