NC_000009.11:g.(?_80919631)_(80923519_?)del AND Neu-Laxova syndrome 2

Germline classification:: Pathogenic (1 submission)
Last evaluated:: Dec 28, 2023
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:: RCV002029708.8

Allele description [Variation Report for NC_000009.11:g.(?_80919631)_(80923519_?)del]

NC_000009.11:g.(?_80919631)_(80923519_?)del

Gene:: PSAT1:phosphoserine aminotransferase 1 [Gene - OMIM - HGNC]
Variant type:: Deletion
Cytogenetic location:: 9q21.2
Genomic location:: Chr9: 80919631 - 80923519 (on Assembly GRCh37)
Preferred name:: NC_000009.11:g.(?_80919631)_(80923519_?)del
HGVS:: NC_000009.11:g.(?_80919631)_(80923519_?)del
This HGVS expression did not pass validation

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
SCV002115736	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Pathogenic (Dec 28, 2023)	germline	clinical testing	PubMed (2) [See all records that cite these PMIDs] 17436247, 28492532

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV002115736

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Pathogenic
(Dec 28, 2023)

germline

clinical testing

PubMed (2)
[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

Sherloc: a comprehensive refinement of the ACMG-AMP variant classification criteria.

Nykamp K, Anderson M, Powers M, Garcia J, Herrera B, Ho YY, Kobayashi Y, Patil N, Thusberg J, Westbrook M; Invitae Clinical Genomics Group, Topper S.

Genet Med. 2017 Oct;19(10):1105-1117. doi: 10.1038/gim.2017.37. Epub 2017 May 11. Erratum in: Genet Med. 2020 Jan;22(1):240. doi: 10.1038/s41436-019-0624-9..

PubMed [citation]

PMID:: 28492532
PMCID:: PMC5632818

Details of each submission

From Labcorp Genetics (formerly Invitae), Labcorp, SCV002115736.4

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (2)

Description

This variant is a gross deletion of the genomic region encompassing exon(s) 4-6 of the PSAT1 gene. This variant would be expected to be in-frame, preserving the integrity of the reading frame. This variant has not been reported in the literature in individuals affected with PSAT1-related conditions. This variant disrupts a region of the PSAT1 protein in which other variant(s) (p.Asp100Ala) have been determined to be pathogenic (PMID: 17436247). This suggests that this is a clinically significant region of the protein, and that variants that disrupt it are likely to be disease-causing. For these reasons, this variant has been classified as Pathogenic.

#	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: Apr 7, 2025

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