Fetal anomalies
Gene: SETD1A

SETD1A (SET domain containing 1A)
EnsemblGeneIds (GRCh38): ENSG00000099381
EnsemblGeneIds (GRCh37): ENSG00000099381
OMIM: 611052, Gene2Phenotype
SETD1A is in 4 panels

3 reviews

Achchuthan Shanmugasundram (Genomics England Curator)

Green List (high evidence)

The rating of this gene has been updated to green following NHS Genomic Medicine Service approval.
Created: 25 Feb 2025, 11:15 a.m. | Last Modified: 25 Feb 2025, 11:15 a.m.

Panel Version: 5.78

This gene and phenotype were reviewed during meetings between November 2024 & January 2025. The meetings included representatives of the Central & South and North Thames R21 testing GLHs and from the R21 Clinical Oversight Group. Clinical review and curation was performed by Stephanie Allen, Natalie Bibb, and Sarah Graham (Central & South GLH), Natalie Chandler and Elizabeth Scotchman (North Thames GLH), and Sunayna Best, Anna De Burca, Natalie Canham, Samantha Doyle, Alice Gardham, Victoria Harrison, Esther Kinning, Sahar Mansour, Soo-Mi Park, and Elizabeth Wall (R21 Clinical Oversight Group).
Created: 20 Feb 2025, 9:40 p.m. | Last Modified: 20 Feb 2025, 9:40 p.m.

Panel Version: 5.16

Mode of inheritance
MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown

Created: 20 Feb 2025, 9:40 p.m.
Last Modified: 20 Feb 2025, 9:40 p.m.
Panel version: 5.78

Stephanie Allen (Birmingham Women's NHS Foundation Trust)

Green List (high evidence)

Green in ID, epilepsy, DDG2P panels. Individuals with SETD1A variants do not show major structural brain defects or severe microcephaly,. Kummeling 2021: 15 patients - global developmental delay and/or intellectual disability, subtle facial dysmorphisms, behavioral and psychiatric problems. Dysmorphic facial features, variable, included high forehead, downslanting palpebral fissures, epicanthal folds, deep-set eyes, wide nose with anteverted nares and broad tip, full cheeks, low-set ears, microtia, full cheeks, everted upper lip, wide mouth, and widely spaced teeth. Many had distal limb anomalies, such as pes planus, broad fingers, or long tapered fingers; joint hypermobility was often present. Additional features present in some patients included gastrointestinal problems, hypotonia. 4 had nonspecific findings on brain imaging, such as abnormal corpus callosum or white matter abnormalities. Jin 2023: case report, baby with congenital bronchomalacia and heart defects including atrial septal defect, patent ductus arteriosus, and pulmonary hypertension, congenital laryngeal stridor, and tracheal stenosis. Zhang case report diagnosed postnatally but enlarged ventricles (0.71.0_cm) were observed during pregnancy without hydrocephalus. Large head circumference (39_cm), hypotonia, facial hemangioma, patent foramen ovale, and hypothyroidism were found after birth. Borderline whether to include as non-specific in pregnancy. No patients prenatally ascertained yet?
Created: 20 Feb 2025, 9:35 p.m. | Last Modified: 20 Feb 2025, 9:35 p.m.

Panel Version: 5.15

Mode of inheritance
MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown

Phenotypes
Neurodevelopmental disorder with speech impairment and dysmorphic facies, MIM#619056

Publications

37000069

Created: 20 Feb 2025, 9:35 p.m.
Last Modified: 20 Feb 2025, 9:35 p.m.
Panel version: 5.15

Rebecca Foulger (Genomics England curator)

I don't know

DDG2P rating in original PAGE list: Probable for INTELLECTUAL DISABILITY
Created: 11 Dec 2018, 9:05 a.m.

Created: 11 Dec 2018, 9:05 a.m.

Panel version: 0.9

Details

Mode of Inheritance

MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown

Sources

Expert Review Green
NHS GMS
PAGE DD-Gene2Phenotype

Phenotypes

Neurodevelopmental disorder with speech impairment and dysmorphic facies, OMIM:619056

OMIM

611052

Clinvar variants

Variants in SETD1A

Penetrance

None

Publications

37000069

Panels with this gene