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  3. PSAT1
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Fetal anomalies

Gene: PSAT1

Green List (high evidence)
PSAT1 (phosphoserine aminotransferase 1)
EnsemblGeneIds (GRCh38): ENSG00000135069
EnsemblGeneIds (GRCh37): ENSG00000135069
OMIM: 610936, Gene2Phenotype
PSAT1 is in 10 panels

6 reviews

Arina Puzriakova (Genomics England Curator)

The rating of this gene has been updated following NHS Genomic Medicine Service approval.
Created: 3 Mar 2022, 11:19 a.m. | Last Modified: 3 Mar 2022, 11:19 a.m.
Panel Version: 1.836
Created: 3 Mar 2022, 11:19 a.m.
Last Modified: 3 Mar 2022, 11:19 a.m.
Panel version: 1.836

Rhiannon Mellis (Great Ormond Street Hospital)

Green List (high evidence)

This gene and phenotype were reviewed during meetings at Great Ormond Street hospital in October 2020. This gene has a Green evidence rating on at least one other related PanelApp panel. Clinical review and curation was performed by Lyn Chitty, Rhiannon Mellis, and Richard Scott. Outcome of review: Confirmed that phenotype is fetally-relevant: add to the Fetal anomalies panel as a Green gene.

Green on related panel(s): Skeletal dysplasia
Created: 28 Jan 2021, 4 p.m. | Last Modified: 28 Jan 2021, 4 p.m.
Panel Version: 1.203

Mode of inheritance
BIALLELIC, autosomal or pseudoautosomal

Phenotypes
Neu-Laxova syndrome 2

Created: 28 Jan 2021, 4 p.m.
Last Modified: 28 Jan 2021, 4 p.m.
Panel version: 1.203

Sarah Leigh (Genomics England Curator)

Green List (high evidence)

There is enough evidence for this gene to be rated GREEN at the next major review.
Created: 20 Aug 2020, 1:18 p.m. | Last Modified: 20 Aug 2020, 1:18 p.m.
Panel Version: 1.88
Created: 20 Aug 2020, 1:18 p.m.
Last Modified: 20 Aug 2020, 1:18 p.m.
Panel version: 1.88

Catherine Snow (Genomics England)

Comment on list classification: Change from Green to Amber, as requested by NHSE for signed-off panel.
Created: 19 Aug 2020, 6:22 p.m. | Last Modified: 19 Aug 2020, 6:22 p.m.
Panel Version: 1.86
Created: 19 Aug 2020, 6:22 p.m.
Last Modified: 19 Aug 2020, 6:22 p.m.
Panel version: 1.86

Zornitza Stark (Australian Genomics)

Green List (high evidence)

6 unrelated families reported; presentation is typically antenatal/neonatal. Microcephaly, cleft palate, oedema are all reported features.
Created: 30 Dec 2019, 7:13 a.m. | Last Modified: 30 Dec 2019, 7:13 a.m.
Panel Version: 1.0

Mode of inheritance
BIALLELIC, autosomal or pseudoautosomal

Phenotypes
Neu-Laxova syndrome 2, MIM# 616038

Publications

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

Created: 30 Dec 2019, 7:13 a.m.
Last Modified: 30 Dec 2019, 7:13 a.m.
Panel version: 1.0

Rebecca Foulger (Genomics England curator)

I don't know

Comment on list classification: Rated 'probable' for Neu-Laxova syndrome in Gene2Phenotype, but there are sufficient cases from the literature to support causation (6 families in PMID:25152457 and 1 Chinese family in PMID:31903955). Therefore updated rating from Amber to Green: Fetally-relevant phenotype and sufficient evidence.
Created: 7 May 2020, 3:41 p.m. | Last Modified: 7 May 2020, 3:41 p.m.
Panel Version: 1.57
PMID:31903955 (Ni et al., 2019) report Chinese Neu-Laxova syndrome (NLS) patients from 2 families. Compound het PSAT1 variants R342W and Y70N were found in the proband from family 1. (PHGDH variants were identified in family 2).
Created: 7 May 2020, 3:31 p.m. | Last Modified: 7 May 2020, 3:31 p.m.
Panel Version: 1.54
PMID:25152457. Acuna-Hidalgo et al., 2014 report a rare AR disorder with severe malformations leading to prenatal or early postnatal lethality (Neu-Laxova syndrome). They identified variants in PHGDH, PSAT1 and PSPH in individuals with NLS, including 6 families with 3 different missense and frameshift PSAT1 variants which segregated with the disease.
Created: 7 May 2020, 3:24 p.m. | Last Modified: 7 May 2020, 3:24 p.m.
Panel Version: 1.54
DDG2P rating in original PAGE list: Probable for PHOSPHOSERINE AMINOTRANSFERASE DEFICIENCY and Probable for NEU-LAXOVA SYNDROME.
Created: 11 Dec 2018, 9:05 a.m.
Created: 11 Dec 2018, 9:05 a.m.

Panel version: 1.54

Details

Mode of Inheritance
BIALLELIC, autosomal or pseudoautosomal
Sources
  • Expert Review Green
  • PAGE DD-Gene2Phenotype
Phenotypes
  • Neu-Laxova syndrome 2, OMIM:616038
  • Neu-Laxova syndrome 2, MONDO:0014466
OMIM
610936
Clinvar variants
Variants in PSAT1
Penetrance
None
Publications
Panels with this gene

History Filter Activity

3 Mar 2022, Gel status: 3

Removed Tag

Arina Puzriakova (Genomics England Curator)

Tag for-review was removed from gene: PSAT1.

3 Mar 2022, Gel status: 3

Added New Source, Status Update

Arina Puzriakova (Genomics England Curator)

Source Expert Review Green was added to PSAT1. Rating Changed from Amber List (moderate evidence) to Green List (high evidence)

1 Feb 2021, Gel status: 2

Set Phenotypes

Arina Puzriakova (Genomics England Curator)

Phenotypes for gene: PSAT1 were changed from Neu-Laxova syndrome 2, 616038; NEU-LAXOVA SYNDROME; PHOSPHOSERINE AMINOTRANSFERASE DEFICIENCY to Neu-Laxova syndrome 2, OMIM:616038; Neu-Laxova syndrome 2, MONDO:0014466

20 Aug 2020, Gel status: 2

Added Tag

Sarah Leigh (Genomics England Curator)

Tag for-review tag was added to gene: PSAT1.

19 Aug 2020, Gel status: 2

Entity classified by Genomics England curator

Catherine Snow (Genomics England)

Gene: psat1 has been classified as Amber List (Moderate Evidence).

7 May 2020, Gel status: 3

Entity classified by Genomics England curator

Rebecca Foulger (Genomics England curator)

Gene: psat1 has been classified as Green List (High Evidence).

7 May 2020, Gel status: 2

Set Phenotypes

Rebecca Foulger (Genomics England curator)

Phenotypes for gene: PSAT1 were changed from NEU-LAXOVA SYNDROME; PHOSPHOSERINE AMINOTRANSFERASE DEFICIENCY to Neu-Laxova syndrome 2, 616038; NEU-LAXOVA SYNDROME; PHOSPHOSERINE AMINOTRANSFERASE DEFICIENCY

7 May 2020, Gel status: 2

Set publications

Rebecca Foulger (Genomics England curator)

Publications for gene: PSAT1 were set to

8 Nov 2018, Gel status: 2

Set Phenotypes

Rebecca Foulger (Genomics England curator)

Added phenotypes NEU-LAXOVA SYNDROME for gene: PSAT1

8 Nov 2018, Gel status: 2

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

Rebecca Foulger (Genomics England curator)

gene: PSAT1 was added gene: PSAT1 was added to Fetal anomalies. Sources: PAGE DD-Gene2Phenotype,Expert Review Amber Mode of inheritance for gene: PSAT1 was set to BIALLELIC, autosomal or pseudoautosomal Phenotypes for gene: PSAT1 were set to PHOSPHOSERINE AMINOTRANSFERASE DEFICIENCY