Is SETD1B p.Pro1582= (c.4746T>G) pathogenic?

SETD1B p.Pro1582= (c.4746T>G) is classified Likely benign in SETD1B (ClinVar, No assertion criteria, 1 submitter; last evaluated 2019-06-24). Ultra-rare (popmax 0.0457%, nfe); Associated with SETD1B-related disorder.

What condition is associated with SETD1B p.Pro1582= (c.4746T>G)?

SETD1B p.Pro1582= (c.4746T>G) is associated with SETD1B-related disorder (ClinVar).

How common is SETD1B p.Pro1582= (c.4746T>G) in the general population?

SETD1B p.Pro1582= (c.4746T>G) is ultra-rare (popmax 0.0457%, nfe) (gnomAD).

SETD1B p.Pro1582=

c.4746T>G · rs1459899756 · VCV3043362

Likely benign No assertion criteria

Classification

Likely benign

ClinVar

Review

No assertion criteria ☆☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

ultra-rare (popmax 0.0457%, nfe)

Conditions

SETD1B-related disorder

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 -5.3	GERP -2.5
Overall
CADD	2.859	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.0457% European (non-Finnish) · 449/983,370 alleles

Filtering AF 0.0421% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.0407%

Overall 0.0368% 485/1,317,404 alleles · ultra-rare exomes 485/1,211,406 · genomes 0/105,998 · joint denominator

Ancestry group	Frequency	1 in
European (non-Finnish)grpmax	0.0457%	2,190
Remaining individualsnot grpmax-eligible	0.033%	3,026
Middle Eastern	0.0256%	3,904
African / African-American	0.0127%	7,867
South Asian	0.00827%	12,094
Ashkenazi Jewishnot grpmax-eligible	0.00799%	12,514
East Asian	0.00563%	17,749
Finnishnot grpmax-eligible	0.00215%	46,532

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: SETD1B
Protein: p.Pro1582=
Coding: c.4746T>G
MANE Select: NM_001353345
dbSNP: rs1459899756
Type: single nucleotide variant
Location: chr12:121823325 (GRCh38)
Gene constraint: LOEUF 0.109 · pLI 1.00 · ClinGen HI 3/3 (gnomAD)
Structure: AlphaFold pLDDT 46.43 · 4 PDB
Residue 1582: the 'disordered' region; a UniProt-annotated variant site (in iddseld)

Full SETD1B gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

SETD1B-related disorder

Similar variants

SETD1B p.Pro1582Leu Uncertain significance ★ ⚠ same residue
SETD1B p.Tyr1943Cys Pathogenic/Likely pathogenic ★★ same condition
SETD1B p.Phe546Leu Uncertain significance ★★ ⚠ same condition
SETD1B c.544+1G>A Likely pathogenic ★ same condition
SETD1B p.Asp1893Asn Likely pathogenic ★ same condition
SETD1B p.Asp1893His Likely pathogenic ★ same condition
SETD1B p.Ala1003Val Uncertain significance ★ ⚠ same condition
SETD1B p.Ala1636Pro Uncertain significance ★ ⚠ same condition

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/setd1b-p-pro1582 (accessed [today's date]).

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