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Hearing loss

Gene: SPATC1L

Amber List (moderate evidence)

SPATC1L (spermatogenesis and centriole associated 1 like)
EnsemblGeneIds (GRCh38): ENSG00000160284
EnsemblGeneIds (GRCh37): ENSG00000160284
OMIM: 612412, Gene2Phenotype
SPATC1L is in 1 panel

2 reviews

Eleanor Williams (Genomics England Curator)

I don't know

Comment on list classification: Promoting from grey to amber. 3 cases reported but only one with segregation data.
Created: 9 Sep 2020, 10:50 a.m. | Last Modified: 9 Sep 2020, 10:50 a.m.
Panel Version: 2.63
Comment on mode of inheritance: I am not sure from the publication about the mode of inheritance. I read it that each family had one variant (no compound hets) and therefore the mode of inheritance would be mono-allelic. However, leaving as both monallelic and biallelic for now due to expert review.
Created: 9 Sep 2020, 10:49 a.m. | Last Modified: 9 Sep 2020, 10:49 a.m.
Panel Version: 2.62
Not associated with a disease phenotype in OMIM.

PMID: 30177775 - Morgan et al 2019 - report a large Italian family affected by early-onset Hereditary hearing loss. After initial screening from 96 known HL genes, exome sequencing was done. A nonsense variant, c.846C>G, p.Tyr282* in SPATC1L was identified. This variant was not described in any public database and was not present in their internal database. It also segregated with HL within the family. They also screened 46 ARHL-candidate genes, including SPATC1L in a cohort of 464 Age related hearing loss (ARHL) patients from inbred and outbred Italian populations and identified two patients with HL and SPATC1L variants (a frameshift duplication c.340_343dupTTCA (p.(Lys115Ilefs*12) in patient Arhl_1, and a missense variant c.656A>C (p.(Tyr219Ser)) in patient Arhl_2). Only one healthy relative was tested in the family of Arhl_1 and found not to have the duplication. No relatives were available for the second family.
Created: 9 Sep 2020, 10:47 a.m. | Last Modified: 9 Sep 2020, 10:47 a.m.
Panel Version: 2.61

Publications

Zornitza Stark (Australian Genomics)

I don't know

Two families with compound het variants, and one family with heterozygous variant and dominant pattern of inheritance described, some functional data.
Sources: Expert list
Created: 2 Jan 2020, 5:28 a.m.

Mode of inheritance
BOTH monoallelic and biallelic, autosomal or pseudoautosomal

Phenotypes
Deafness

Publications

Details

Mode of Inheritance
BOTH monoallelic and biallelic, autosomal or pseudoautosomal
Sources
  • Expert Review Amber
Phenotypes
  • Deafness
OMIM
612412
Clinvar variants
Variants in SPATC1L
Penetrance
None
Publications
Panels with this gene

History Filter Activity

9 Sep 2020, Gel status: 2

Entity classified by Genomics England curator

Eleanor Williams (Genomics England Curator)

Gene: spatc1l has been classified as Amber List (Moderate Evidence).

9 Sep 2020, Gel status: 0

Set mode of inheritance

Eleanor Williams (Genomics England Curator)

Mode of inheritance for gene: SPATC1L was changed from BOTH monoallelic and biallelic, autosomal or pseudoautosomal to BOTH monoallelic and biallelic, autosomal or pseudoautosomal

2 Jan 2020, Gel status: 0

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

Zornitza Stark (Australian Genomics)

gene: SPATC1L was added gene: SPATC1L was added to Hearing loss. Sources: Expert list Mode of inheritance for gene: SPATC1L was set to BOTH monoallelic and biallelic, autosomal or pseudoautosomal Publications for gene: SPATC1L were set to 30177775 Phenotypes for gene: SPATC1L were set to Deafness