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Intellectual disability

Gene: SPATA5L1

Green List (high evidence)
SPATA5L1 (spermatogenesis associated 5 like 1)
EnsemblGeneIds (GRCh38): ENSG00000171763
EnsemblGeneIds (GRCh37): ENSG00000171763
SPATA5L1 is in 8 panels

4 reviews

Achchuthan Shanmugasundram (Genomics England Curator)

Added new-gene-name tag, new approved HGNC gene symbol for SPATA5L1 is AFG2B.
Created: 16 Oct 2023, 6:16 p.m. | Last Modified: 16 Oct 2023, 6:16 p.m.
Panel Version: 5.313
Created: 16 Oct 2023, 6:16 p.m.
Last Modified: 16 Oct 2023, 6:16 p.m.
Panel version: 5.313

Arina Puzriakova (Genomics England Curator)

Green List (high evidence)

The rating of this gene has been updated to Green following NHS Genomic Medicine Service approval.
Created: 30 Jan 2023, 5:50 p.m. | Last Modified: 30 Jan 2023, 5:50 p.m.
Panel Version: 4.53
Created: 30 Jan 2023, 5:50 p.m.
Last Modified: 30 Jan 2023, 5:50 p.m.
Panel version: 4.53

Ivone Leong (Genomics England Curator)

Comment on list classification: New gene added by Zornitza Stark (Australian Genomics). This gene is associated with a phenotype in OMIM and Gene2Phenotype (limited). There is enough evidence to support a gene-disease association, this gene should be rated Green.
Created: 11 Jan 2022, 11:41 a.m. | Last Modified: 11 Jan 2022, 11:41 a.m.
Panel Version: 3.1491
Created: 11 Jan 2022, 11:41 a.m.
Last Modified: 11 Jan 2022, 11:41 a.m.
Panel version: 3.1491

Zornitza Stark (Australian Genomics)

Green List (high evidence)

47 individuals from 26 unrelated families from various ethnicities with biallelic variants reported. Phenotypes include ID, hearing impairment, movement disorder, abnormal MRI, hypotonia, visual impairment, epilepsy, and microcephaly.

~53% of patients had ID.
Sources: Literature
Created: 4 Dec 2021, 7:41 a.m.

Mode of inheritance
BIALLELIC, autosomal or pseudoautosomal

Phenotypes
Neurodevelopmental disorder with hearing loss and spasticity, MIM# 619616

Publications

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

Created: 4 Dec 2021, 7:41 a.m.

Panel version: 3.1478

Details

Mode of Inheritance
BIALLELIC, autosomal or pseudoautosomal
Sources
  • Expert Review Green
  • NHS GMS
Phenotypes
  • Neurodevelopmental disorder with hearing loss and spasticity, OMIM:619616
Tags
new-gene-name gene-checked
Clinvar variants
Variants in SPATA5L1
Penetrance
None
Publications
Panels with this gene

History Filter Activity

2 Oct 2023, Gel status: 3

Added Tag

Achchuthan Shanmugasundram (Genomics England Curator)

Tag new-gene-name tag was added to gene: SPATA5L1.

8 Feb 2023, Gel status: 3

Added Tag

Eleanor Williams (Genomics England Curator)

Tag gene-checked tag was added to gene: SPATA5L1.

31 Jan 2023, Gel status: 3

Removed Tag

Arina Puzriakova (Genomics England Curator)

Tag Q1_22_rating was removed from gene: SPATA5L1.

30 Jan 2023, Gel status: 3

Added New Source, Added New Source, Status Update

Arina Puzriakova (Genomics England Curator)

Source NHS GMS was added to SPATA5L1. Source Expert Review Green was added to SPATA5L1. Rating Changed from Amber List (moderate evidence) to Green List (high evidence)

11 Jan 2022, Gel status: 2

Entity classified by Genomics England curator

Ivone Leong (Genomics England Curator)

Gene: spata5l1 has been classified as Amber List (Moderate Evidence).

11 Jan 2022, Gel status: 0

Added Tag

Ivone Leong (Genomics England Curator)

Tag Q1_22_rating tag was added to gene: SPATA5L1.

11 Jan 2022, Gel status: 0

Set Phenotypes

Ivone Leong (Genomics England Curator)

Phenotypes for gene: SPATA5L1 were changed from Neurodevelopmental disorder with hearing loss and spasticity, MIM# 619616 to Neurodevelopmental disorder with hearing loss and spasticity, OMIM:619616

4 Dec 2021, Gel status: 0

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

Zornitza Stark (Australian Genomics)

gene: SPATA5L1 was added gene: SPATA5L1 was added to Intellectual disability. Sources: Literature Mode of inheritance for gene: SPATA5L1 was set to BIALLELIC, autosomal or pseudoautosomal Publications for gene: SPATA5L1 were set to 34626583 Phenotypes for gene: SPATA5L1 were set to Neurodevelopmental disorder with hearing loss and spasticity, MIM# 619616 Review for gene: SPATA5L1 was set to GREEN gene: SPATA5L1 was marked as current diagnostic