Is SETD1A p.Pro614= (c.1842T>A) pathogenic?

SETD1A p.Pro614= (c.1842T>A) is classified Likely benign in SETD1A (ClinVar, No assertion criteria, 1 submitter; last evaluated 2019-09-23). No allele count reported in gnomAD v4.1 (AN 912,386); Associated with SETD1A-related disorder.

What condition is associated with SETD1A p.Pro614= (c.1842T>A)?

SETD1A p.Pro614= (c.1842T>A) is associated with SETD1A-related disorder (ClinVar).

How common is SETD1A p.Pro614= (c.1842T>A) in the general population?

SETD1A p.Pro614= (c.1842T>A) is no allele count reported in gnomAD v4.1 (AN 912,386) (gnomAD).

SETD1A p.Pro614=

c.1842T>A · rs774184477 · VCV3040056

Likely benign No assertion criteria

Classification

Likely benign

ClinVar

Review

No assertion criteria ☆☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Not reported

no allele count reported in gnomAD v4.1 (AN 912,386)

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 -6	GERP -3.6
Overall
CADD	0.086	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

No allele count reported in gnomAD v4.1 (AN 912,386). This is missing data, not an absence: the variant may or may not be present in gnomAD. Rarity (ACMG PM2) and BA1/BS1 cannot be assessed for it.

Variant & gene context

Gene: SETD1A
Protein: p.Pro614=
Coding: c.1842T>A
MANE Select: NM_014712
dbSNP: rs774184477
Type: single nucleotide variant
Location: chr16:30965723 (GRCh38)
Gene constraint: LOEUF 0.279 · pLI 1.00 · ClinGen HI 3/3 (gnomAD)
Structure: AlphaFold pLDDT 49.20 · 4 PDB
Residue 614: a UniProt-annotated variant site (in nedsid); the 'disordered' region

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

Disease context

SETD1A-related disorder

Similar variants

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
SETD1A p.Gly1139Glu 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-pro614 (accessed [today's date]).

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