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Intellectual disability syndromic and non-syndromic

Gene: SPEN

Green List (high evidence)

SPEN (spen family transcriptional repressor)
EnsemblGeneIds (GRCh38): ENSG00000065526
EnsemblGeneIds (GRCh37): ENSG00000065526
OMIM: 613484, Gene2Phenotype
SPEN is in 7 panels

2 reviews

Chern Lim (Victorian Clinical Genetics Services)

Green List (high evidence)

PMID: 33596411
- 34 individuals with truncating variants in SPEN reported, most are de novo variants.
- Clinical profile includes developmental delay/intellectual disability, autism spectrum disorder, anxiety, aggressive behavior, attention deficit disorder, hypotonia, brain and spine anomalies, congenital heart defects, high/narrow palate, facial dysmorphisms, and obesity/increased BMI, especially in females.
- Authors showed haploinsufficiency of SPEN is associated with a distinctive DNA methylation episignature of the X chromosome in affected females.
Created: 1 Mar 2021, 4:31 a.m. | Last Modified: 1 Mar 2021, 4:31 a.m.
Panel Version: 0.3466

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

Phenotypes
Developmental delay/intellectual disability, autism spectrum disorder, anxiety, aggressive behavior, attention deficit disorder, hypotonia, brain and spine anomalies, congenital heart defects, high/narrow palate, facial dysmorphisms, and obesity/increased BMI

Publications

Variants in this GENE are reported as part of current diagnostic practice

Zornitza Stark (Victorian Clinical Genetics Services; Australian Genomics)

I don't know

PMID: 33057194 - Has been identified as a gene with significant de novo enrichment in a large trio study from the Deciphering Developmental Disorders study. 25 de novo variants (6 frameshift, 1 in-frame, 7 missense, 8 stopgain, 3 synonymous) identified in ~10,000 cases with developmental disorders (no other phenotype info provided hence Amber rating).
Sources: Literature
Created: 4 Nov 2020, 5:25 a.m.

Mode of inheritance
MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted

Phenotypes
Developmental disorders

Publications

Details

Mode of Inheritance
MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted
Sources
  • Expert Review Green
  • Literature
Phenotypes
  • Radio-Tartaglia syndrome, MIM# 619312
  • Intellectual disability
  • autism
  • congenital anomalies
OMIM
613484
Clinvar variants
Variants in SPEN
Penetrance
None
Publications
Panels with this gene

History Filter Activity

12 May 2021, Gel status: 3

Set publications

Zornitza Stark (Victorian Clinical Genetics Services; Australian Genomics)

Publications for gene: SPEN were set to 33057194

12 May 2021, Gel status: 3

Set Phenotypes

Zornitza Stark (Victorian Clinical Genetics Services; Australian Genomics)

Phenotypes for gene: SPEN were changed from Intellectual disability; autism; congenital anomalies to Radio-Tartaglia syndrome, MIM# 619312; Intellectual disability; autism; congenital anomalies

1 Mar 2021, Gel status: 3

Set Phenotypes

Zornitza Stark (Victorian Clinical Genetics Services; Australian Genomics)

Phenotypes for gene: SPEN were changed from Developmental disorders to Intellectual disability; autism; congenital anomalies

1 Mar 2021, Gel status: 3

Entity classified by Genomics England curator

Alison Yeung (Victorian Clinical Genetics Services)

Gene: spen has been classified as Green List (High Evidence).

1 Mar 2021, Gel status: 3

Entity classified by Genomics England curator

Alison Yeung (Victorian Clinical Genetics Services)

Gene: spen has been classified as Green List (High Evidence).

4 Nov 2020, Gel status: 2

Entity classified by Genomics England curator

Zornitza Stark (Victorian Clinical Genetics Services; Australian Genomics)

Gene: spen has been classified as Amber List (Moderate Evidence).

4 Nov 2020, Gel status: 2

Entity classified by Genomics England curator

Zornitza Stark (Victorian Clinical Genetics Services; Australian Genomics)

Gene: spen has been classified as Amber List (Moderate Evidence).

4 Nov 2020, Gel status: 1

Created, Added New Source, Set mode of inheritance, Set publications, Set Phenotypes

Zornitza Stark (Victorian Clinical Genetics Services; Australian Genomics)

gene: SPEN was added gene: SPEN was added to Intellectual disability syndromic and non-syndromic. Sources: Literature Mode of inheritance for gene: SPEN was set to MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted Publications for gene: SPEN were set to 33057194 Phenotypes for gene: SPEN were set to Developmental disorders Review for gene: SPEN was set to AMBER