Tubulointerstitial kidney disease

Gene: SEC61A1

Amber List (moderate evidence)

SEC61A1 (Sec61 translocon alpha 1 subunit)
EnsemblGeneIds (GRCh38): ENSG00000058262
EnsemblGeneIds (GRCh37): ENSG00000058262
OMIM: 609213, Gene2Phenotype
SEC61A1 is in 7 panels

3 reviews

Arina Puzriakova (Genomics England Curator)

Comment on list classification: Changed rating from Green to Amber so that Green genes on this panel reflect the NHS signed-off version. This will be reviewed at the next GMS panel update (added 'for-review' tag).
Created: 20 Oct 2020, 4:09 p.m. | Last Modified: 20 Oct 2020, 4:09 p.m.
Panel Version: 1.11

Zornitza Stark (Australian Genomics)

Green List (high evidence)

We agree there are sufficient cases reported to upgrade to Green.
Created: 23 Jan 2020, 4:12 a.m. | Last Modified: 23 Jan 2020, 4:12 a.m.
Panel Version: 1.0

Mode of inheritance
MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted

Phenotypes
Familial juvenile Hyperuricemic nephropathy-4 MIM 617056

Publications

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

Eleanor Williams (Genomics England Curator)

Green List (high evidence)

Comment on list classification: Changing rating from Amber to Green. Two familial cases reported in Bolar publication plus animal model. Further case reported in Groopman.
Created: 23 Mar 2020, 1:14 p.m. | Last Modified: 23 Mar 2020, 1:14 p.m.
Panel Version: 1.9
PMID: 30586318 - Groopman et al 2019 - Patient CKD184 in Table S7 has a heterozygous missense variant p.I428M in SEC61A1. The genetic diagnosis was Hyperuricemic nephropathy familial juvenile 4.

PMID: 27392076 Bolar et al 2016 - report on two families with ADTKD and congenital anemia accompanied by either intrauterine growth retardation or neutropenia. Exclusion of known ADTKD genes coupled with linkage analysis, whole-exome sequencing, and targeted re-sequencing identified heterozygous missense variants in SEC61A1-c.553A>G (p.Thr185Ala) and c.200T>G (p.Val67Gly). Zebrafish model re-capitulated the phenotype and could not be rescued by mRNA with the pathogenic alleles.
Created: 23 Mar 2020, 1:12 p.m. | Last Modified: 23 Mar 2020, 1:12 p.m.
Panel Version: 1.7
Upgrading review rating to green, the Groopman paper increases the number of cases to 3.
Created: 13 Nov 2019, 12:23 p.m. | Last Modified: 13 Nov 2019, 12:23 p.m.
Panel Version: 1.0
Further case reported in Groopman et al 2019 (PMID: 30586318)
Created: 11 Sep 2019, 12:55 p.m. | Last Modified: 11 Sep 2019, 12:55 p.m.
Panel Version: 1.0
This gene was part of an initial gene list collated by Emma Ashton (NE Thames Regional Genetics laboratory, GOSH NHS Foundation Trust) January 2019 on behalf of the GMS Renal Specialist Test Group.Gene Symbol submitted:SEC61A1;Suggested initial gene rating: Amber;Evidence for inclusion: none provided;Evidence for exclusion:Suggested phenocopy;Technical notes (e.g. non-coding/CNV mutations requiring coverage?): none provided
Created: 2 Feb 2019, 12:48 a.m.

Mode of inheritance
MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted

Phenotypes
Familial juvenile Hyperuricemic nephropathy-4 MIM 617056

Details

Mode of Inheritance
MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted
Sources
  • Expert Review Amber
  • NHS GMS
Phenotypes
  • Familial juvenile Hyperuricemic nephropathy-4 MIM 617056
Tags
for-review
OMIM
609213
Clinvar variants
Variants in SEC61A1
Penetrance
None
Publications
Panels with this gene

History Filter Activity

20 Oct 2020, Gel status: 2

Entity classified by Genomics England curator

Arina Puzriakova (Genomics England Curator)

Gene: sec61a1 has been classified as Amber List (Moderate Evidence).

24 Jun 2020, Gel status: 3

Added Tag

Eleanor Williams (Genomics England Curator)

Tag for-review tag was added to gene: SEC61A1.

23 Mar 2020, Gel status: 3

Entity classified by Genomics England curator

Eleanor Williams (Genomics England Curator)

Gene: sec61a1 has been classified as Green List (High Evidence).

23 Mar 2020, Gel status: 2

Set publications

Eleanor Williams (Genomics England Curator)

Publications for gene: SEC61A1 were set to

2 Feb 2019, Gel status: 2

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

Eleanor Williams (Genomics England Curator)

gene: SEC61A1 was added gene: SEC61A1 was added to Tubulointerstitial kidney disease. Sources: Expert Review Amber,NHS GMS Mode of inheritance for gene: SEC61A1 was set to MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted Phenotypes for gene: SEC61A1 were set to Familial juvenile Hyperuricemic nephropathy-4 MIM 617056