NM_058179.4(PSAT1):c.868G>A (p.Val290Ile) AND Neu-Laxova syndrome 2

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Aug 15, 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:: RCV000818408.6

Allele description [Variation Report for NM_058179.4(PSAT1):c.868G>A (p.Val290Ile)]

NM_058179.4(PSAT1):c.868G>A (p.Val290Ile)

Gene:

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

Variant type:

single nucleotide variant

Cytogenetic location:

9q21.2

Genomic location:

Preferred name:

NM_058179.4(PSAT1):c.868G>A (p.Val290Ile)

HGVS:

NC_000009.12:g.78317803G>A
NG_012165.1:g.25661G>A
NM_021154.5:c.868G>A
NM_058179.4:c.868G>AMANE SELECT
NP_066977.1:p.Val290Met
NP_478059.1:p.Val290Ile
NC_000009.11:g.80932719G>A
NM_058179.3:c.868G>A

Protein change:

V290I

Links:

dbSNP: rs200049723

NCBI 1000 Genomes Browser:

rs200049723

Molecular consequence:

NM_021154.5:c.868G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_058179.4:c.868G>A - missense variant - [Sequence Ontology: SO:0001583]

Functional consequence:

function_uncertain_variant [Sequence Ontology: SO:0002220] - Comment(s)
- Impaired relative to wildtype, but less than all known disease alleles. PMID:32077105 Table S7.
mutation affecting coding sequence [Sequence Ontology: SO:1000054] - Comment(s)
- Impaired relative to wildtype, but less than all known disease alleles. PMID:32077105 Table S7.

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
SCV000959019	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (Aug 15, 2022)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000959019

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(Aug 15, 2022)

germline

clinical testing

PubMed (1)
[See all records that cite this PMID]

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

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, SCV000959019.5

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

Description

This sequence change replaces valine, which is neutral and non-polar, with isoleucine, which is neutral and non-polar, at codon 290 of the PSAT1 protein (p.Val290Ile). This variant is present in population databases (rs200049723, gnomAD 0.02%). This variant has not been reported in the literature in individuals affected with PSAT1-related conditions. ClinVar contains an entry for this variant (Variation ID: 661070). Algorithms developed to predict the effect of missense changes on protein structure and function output the following: SIFT: "Tolerated"; PolyPhen-2: "Benign"; Align-GVGD: "Class C0". The isoleucine amino acid residue is found in multiple mammalian species, which suggests that this missense change does not adversely affect protein function. In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance.

#	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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