Is SETD1A p.Glu857= (c.2571G>A) pathogenic?

SETD1A p.Glu857= (c.2571G>A) is classified Likely benign in SETD1A (ClinVar, No assertion criteria, 1 submitter; last evaluated 2019-07-11). Ultra-rare (popmax 0.0332%, mid); Associated with SETD1A-related disorder.

What condition is associated with SETD1A p.Glu857= (c.2571G>A)?

SETD1A p.Glu857= (c.2571G>A) is associated with SETD1A-related disorder (ClinVar).

How common is SETD1A p.Glu857= (c.2571G>A) in the general population?

SETD1A p.Glu857= (c.2571G>A) is ultra-rare (popmax 0.0332%, mid) (gnomAD).

SETD1A p.Glu857=

c.2571G>A · rs142914701 · VCV3049718

Likely benign No assertion criteria

Classification

Likely benign

ClinVar

Review

No assertion criteria ☆☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

ultra-rare (popmax 0.0332%, mid)

Conditions

SETD1A-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 0.58	GERP -4.5, phastCons 0.99
Overall
CADD	5.237	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.0332% Middle Eastern · 2/6,028 alleles

Filtering AF 0.0221% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.0188%

Overall 0.00183% 29/1,582,180 alleles · ultra-rare exomes 14/1,429,850 · genomes 15/152,330 · joint denominator

Ancestry group	Frequency	1 in
Middle Easterngrpmax	0.0332%	3,014
African / African-American	0.0322%	3,109
Remaining individualsnot grpmax-eligible	0.00489%	20,462

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: SETD1A
Protein: p.Glu857=
Coding: c.2571G>A
MANE Select: NM_014712
dbSNP: rs142914701
Type: single nucleotide variant
Location: chr16:30966949 (GRCh38)
Gene constraint: LOEUF 0.279 · pLI 1.00 · ClinGen HI 3/3 (gnomAD)
Structure: AlphaFold pLDDT 49.20 · 4 PDB
Residue 857: a UniProt-annotated variant site (in nedsid)

Full SETD1A gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

SETD1A-related disorder

Similar variants

SETD1A p.Glu857Ter Likely pathogenic ★ same residue
SETD1A p.Leu669Phe Uncertain significance ★★ ⚠ same condition
SETD1A p.Pro449Ala Uncertain significance ★★ ⚠ same condition
SETD1A p.Cys1697Arg Likely pathogenic ★ same condition
SETD1A p.Glu1345Ter Likely pathogenic ★ same condition
SETD1A p.Glu982Ter Pathogenic ★ same condition
SETD1A c.247-2A>C Uncertain significance ★ same condition
SETD1A p.Ala472Val 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/setd1a-p-glu857 (accessed [today's date]).

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