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Intellectual disability

Gene: SPATA5

Green List (high evidence)
SPATA5 (spermatogenesis associated 5)
EnsemblGeneIds (GRCh38): ENSG00000145375
EnsemblGeneIds (GRCh37): ENSG00000145375
OMIM: 613940, Gene2Phenotype
SPATA5 is in 7 panels

4 reviews

Achchuthan Shanmugasundram (Genomics England Curator)

Added new-gene-name tag, new approved HGNC gene symbol for SPATA5 is AFG2A.
Created: 16 Oct 2023, 6:18 p.m. | Last Modified: 16 Oct 2023, 6:18 p.m.
Panel Version: 5.313
Created: 16 Oct 2023, 6:18 p.m.
Last Modified: 16 Oct 2023, 6:18 p.m.
Panel version: 5.313

Rachel Jones (GSTT)

Green List (high evidence)

Comment on list classification: As per review, multiple patients with ID, epilepsy and hearing loss with biallelic SPATA5 variants I several published papers.
Created: 11 Jun 2018, 11:06 a.m.
Comment on list classification: As per review, multiple patients with ID, epilepsy and hearing loss with biallelic SPATA5 variants I several published papers.
Created: 11 Jun 2018, 11:06 a.m.
Tanaka et al PMID: 26299366 identified "14 individuals [from 10 families] with microcephaly, developmental delay, intellectual disability, hypotonia, spasticity, seizures, sensorineural hearing loss, cortical visual impairment, and rare autosomal-recessive predicted pathogenic variants" in SPATA5

Puussep et al PMID: 29343804 describes 5 further patients "with psychomotor developmental delay, microcephaly, epilepsy and hearing impairment, who were thought clinically to have a mitochondrial disease with subsequent whole-exome sequencing analysis detecting compound heterozygous variants in the SPATA5 gene"
Created: 11 Jun 2018, 10:07 a.m.

Mode of inheritance
BIALLELIC, autosomal or pseudoautosomal

Phenotypes
Epilepsy, hearing loss, and mental retardation syndrome 616577

Publications

Created: 11 Jun 2018, 10:07 a.m.

Panel version: 2.96

BRIDGE consortium (NIHRBR-RD)

Green List (high evidence)

This is a pertinent gene from the NIHR BioResource - Rare Diseases Study (NIHRBR-RD) BRIDGE Study : SPEED (Specialist Pathology: Evaluating Exomes in Diagnostics) which covers epilepsies, movement and microcephaly disorders, this gene is on the SPEED_NEURO_20170705 gene list. Evidences used for SPEED NEURO gene list: in_ddg2p_2_4_2017;in_ddg2p_2_4_2017_conf . Main mutation mechanism : NA
Created: 27 Jul 2017, 8:32 p.m.

Mode of inheritance
Unknown

Publications

Created: 2 Aug 2017, 10:53 p.m.

Panel version: 1.354

Louise Daugherty (Genomics England Curator)

Comment on mode of inheritance: changed MOI as recommended by external reviewer
Created: 11 Jun 2018, 4:10 p.m.
Comment on publications: Added publications from expert review
Created: 11 Jun 2018, 4:04 p.m.
Comment on list classification: changed from Amber to Green due to expert review and publications supporting the ID phenotype
Created: 11 Jun 2018, 4:03 p.m.
Comment on phenotypes: Added phenotype from expert review
Created: 11 Jun 2018, 4:02 p.m.
Comment on list classification: This gene is from an expert list and needs further assessment by the Genomics England curation team to access inclusion and pertinence to this panel.
Created: 28 Jul 2017, 5:16 p.m.
Created: 28 Jul 2017, 5:16 p.m.

Panel version: 1.353

Details

Mode of Inheritance
BIALLELIC, autosomal or pseudoautosomal
Sources
  • Expert Review Green
Phenotypes
  • Neurodevelopmental disorder with hearing loss, seizures, and brain abnormalities, OMIM:616577
Tags
new-gene-name
OMIM
613940
Clinvar variants
Variants in SPATA5
Penetrance
Complete
Publications
Panels with this gene

History Filter Activity

12 Mar 2024, Gel status: 3

Set Phenotypes

Arina Puzriakova (Genomics England Curator)

Phenotypes for gene: SPATA5 were changed from Epilepsy, hearing loss, and mental retardation syndrome, 616577 to Neurodevelopmental disorder with hearing loss, seizures, and brain abnormalities, OMIM:616577

2 Oct 2023, Gel status: 3

Added Tag

Achchuthan Shanmugasundram (Genomics England Curator)

Tag new-gene-name tag was added to gene: SPATA5.

11 Jun 2018, Gel status: 3

Set Phenotypes

Louise Daugherty (Genomics England Curator)

Phenotypes for gene: SPATA5 were set to Epilepsy, hearing loss, and mental retardation syndrome, 616577

11 Jun 2018, Gel status: 3

Set mode of inheritance

Louise Daugherty (Genomics England Curator)

Mode of inheritance for gene: SPATA5 was changed from BIALLELIC, autosomal or pseudoautosomal to BIALLELIC, autosomal or pseudoautosomal

11 Jun 2018, Gel status: 3

Set mode of inheritance

Louise Daugherty (Genomics England Curator)

Mode of inheritance for gene: SPATA5 was changed from Unknown to BIALLELIC, autosomal or pseudoautosomal

11 Jun 2018, Gel status: 3

Set publications

Louise Daugherty (Genomics England Curator)

Publications for gene: SPATA5 were set to 26299366; 29343804; 25529582

11 Jun 2018, Gel status: 3

Set publications

Louise Daugherty (Genomics England Curator)

Publications for gene: SPATA5 were set to 26299366; 29343804; 25529582

11 Jun 2018, Gel status: 3

Entity classified by Genomics England curator

Louise Daugherty (Genomics England Curator)

Gene: spata5 has been classified as Green List (High Evidence).

11 Jun 2018, Gel status: 2

Set Phenotypes

Louise Daugherty (Genomics England Curator)

Phenotypes for gene: SPATA5 were set to Epilepsy, hearing loss, and mental retardation syndrome, 616577

11 Jun 2018, Gel status: 2

Set publications

Louise Daugherty (Genomics England Curator)

Publications for gene: SPATA5 were set to 26299366; 29343804; 25529582

12 Mar 2018, Gel status: 2

Panel promoted to version 2.0

Ellen McDonagh (Genomics England Curator)

12.03.2018: Due to major updates completed (Phase 1, 2 and 3), this panel was promoted to Version 2 in order to reflect the major updates since November 2017 which have resulted in reviews for 836 genes added by Genomics England Curators and the Clinical Team, 130 new Green genes added to the interpretation pipeline (from 751 to 881 Green genes), and the gene total has increased from 1879 to 1927.

28 Jul 2017, Gel status: 2

Gene classified by Genomics England curator

Louise Daugherty (Genomics England Curator)

This gene has been classified as Amber List (Moderate Evidence).

27 Jul 2017, Gel status: 0

Added New Source

BRIDGE consortium (NIHRBR-RD)

SPATA5 was added to Intellectual disabilitypanel. Sources: BRIDGE study SPEED NEURO Tier1 Gene

27 Jul 2017, Gel status: 0

Created

BRIDGE consortium (NIHRBR-RD)

SPATA5 was created by BRIDGE