NM_058179.4(PSAT1):c.82_83del (p.Glu28fs) AND Neu-Laxova syndrome 2

Germline classification:: Pathogenic (1 submission)
Last evaluated:: Sep 30, 2022
Review status:: 1 star out of maximum of 4 stars
criteria provided, single submitter

Somatic classification of clinical impact:: None
Review status:: (0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided

Somatic classification of oncogenicity:: None
Review status:: (0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided

Record status:: current
Accession:: RCV002952911.4

Allele description [Variation Report for NM_058179.4(PSAT1):c.82_83del (p.Glu28fs)]

NM_058179.4(PSAT1):c.82_83del (p.Glu28fs)

Gene:

PSAT1:phosphoserine aminotransferase 1 [Gene - OMIM - HGNC]

Variant type:

Deletion

Cytogenetic location:

9q21.2

Genomic location:

Preferred name:

NM_058179.4(PSAT1):c.82_83del (p.Glu28fs)

HGVS:

NC_000009.12:g.78300623_78300624del
NG_012165.1:g.8481_8482del
NM_021154.5:c.82_83del
NM_058179.4:c.82_83delMANE SELECT
NP_066977.1:p.Glu28fs
NP_478059.1:p.Glu28fs
NC_000009.11:g.80915539_80915540del

Protein change:

E28fs

Links:

dbSNP: rs2489629517

NCBI 1000 Genomes Browser:

rs2489629517

Molecular consequence:

NM_021154.5:c.82_83del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_058179.4:c.82_83del - frameshift variant - [Sequence Ontology: SO:0001589]

Condition(s)

Name:: Neu-Laxova syndrome 2
Identifiers:: MONDO: MONDO:0014466; MedGen: C4015019; Orphanet: 2671; OMIM: 616038

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV003273276	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Pathogenic (Sep 30, 2022)	germline	clinical testing	PubMed (3) [See all records that cite these PMIDs] 17436247, 25152457, 28492532

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV003273276

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Pathogenic
(Sep 30, 2022)

germline

clinical testing

PubMed (3)
[See all records that cite these PMIDs]

Help

Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	germline	unknown	not provided	not provided	not provided	not provided	not provided	clinical testing

Citations

PubMed

Phosphoserine aminotransferase deficiency: a novel disorder of the serine biosynthesis pathway.

Hart CE, Race V, Achouri Y, Wiame E, Sharrard M, Olpin SE, Watkinson J, Bonham JR, Jaeken J, Matthijs G, Van Schaftingen E.

Am J Hum Genet. 2007 May;80(5):931-7. Epub 2007 Mar 30.

PubMed [citation]

PMID:: 17436247
PMCID:: PMC1852735

Neu-Laxova syndrome is a heterogeneous metabolic disorder caused by defects in enzymes of the L-serine biosynthesis pathway.

Acuna-Hidalgo R, Schanze D, Kariminejad A, Nordgren A, Kariminejad MH, Conner P, Grigelioniene G, Nilsson D, Nordenskjöld M, Wedell A, Freyer C, Wredenberg A, Wieczorek D, Gillessen-Kaesbach G, Kayserili H, Elcioglu N, Ghaderi-Sohi S, Goodarzi P, Setayesh H, van de Vorst M, Steehouwer M, Pfundt R, et al.

Am J Hum Genet. 2014 Sep 4;95(3):285-93. doi: 10.1016/j.ajhg.2014.07.012. Epub 2014 Aug 21.

PubMed [citation]

PMID:: 25152457
PMCID:: PMC4157144

See all PubMed Citations (3)

Details of each submission

From Labcorp Genetics (formerly Invitae), Labcorp, SCV003273276.3

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (3)

Description

For these reasons, this variant has been classified as Pathogenic. This variant has not been reported in the literature in individuals affected with PSAT1-related conditions. This variant is not present in population databases (gnomAD no frequency). This sequence change creates a premature translational stop signal (p.Glu28Ilefs*10) in the PSAT1 gene. It is expected to result in an absent or disrupted protein product. Loss-of-function variants in PSAT1 are known to be pathogenic (PMID: 17436247, 25152457).

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	unknown	not provided	not provided	not provided		not provided	not provided	not provided	not provided

Last Updated: May 16, 2025

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