NM_058179.4(PSAT1):c.367A>G (p.Ile123Val) AND not provided

Clinical significance:Likely benign

Review status:(0/4) 0 stars out of maximum of 4 stars

no assertion criteria provided

Based on:
2 submissions [Details]
Record status:
current
Accession:
RCV001254501.2

Allele description [Variation Report for NM_058179.4(PSAT1):c.367A>G (p.Ile123Val)]

NM_058179.4(PSAT1):c.367A>G (p.Ile123Val)

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.367A>G (p.Ile123Val)
HGVS:
  • NC_000009.12:g.78304910A>G
  • NG_012165.1:g.12768A>G
  • NM_021154.5:c.367A>G
  • NM_058179.4:c.367A>GMANE SELECT
  • NP_066977.1:p.Ile123Val
  • NP_478059.1:p.Ile123Val
  • NC_000009.11:g.80919826A>G
  • NM_058179.3:c.367A>G
Protein change:
I123V
Links:
dbSNP: rs116577685
NCBI 1000 Genomes Browser:
rs116577685
Molecular consequence:
  • NM_021154.5:c.367A>G - missense variant - [Sequence Ontology: SO:0001583]
  • NM_058179.4:c.367A>G - missense variant - [Sequence Ontology: SO:0001583]
Functional consequence:
  • functionally_normal [Sequence Ontology: SO:0002219] - Comment(s)
  • mutation affecting coding sequence [Sequence Ontology: SO:1000054] - Comment(s)

Condition(s)

Identifiers:
MedGen: CN517202

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV001430480Dudley Research Group,Pacific Northwest Research Instituteno assertion providednot providedunknown, not applicableresearch, in vivo

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

SCV001550285Department of Pathology and Laboratory Medicine,Sinai Health System - The Canadian Open Genetics Repository (COGR)

See additional submitters

no assertion criteria providedLikely benignunknownclinical testing

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedunknownyesnot providednot providednot providednot providednot providedclinical testing
not providednot applicablenot applicablenot providednot providednot providednot providednot providedin vivo
not providedunknownunknownnot providednot providednot providednot providednot providedresearch

Citations

PubMed

A yeast-based complementation assay elucidates the functional impact of 200 missense variants in human PSAT1.

Sirr A, Lo RS, Cromie GA, Scott AC, Ashmead J, Heyesus M, Dudley AM.

J Inherit Metab Dis. 2020 Jul;43(4):758-769. doi: 10.1002/jimd.12227. Epub 2020 Feb 27.

PubMed [citation]
PMID:
32077105
PMCID:
PMC7444316

Details of each submission

From Dudley Research Group,Pacific Northwest Research Institute, SCV001430480.2

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedresearch PubMed (1)
2not providednot providednot providednot providedin vivo PubMed (1)
3not providednot providednot providednot providedin vivo PubMed (1)

Description

"Not impaired in assay relative to wildtype."
"Not impaired in assay relative to wildtype."
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1unknownunknownnot providednot providednot providednot providednot providednot providednot provided
2not applicablenot applicablenot providednot providednot providednot providednot providednot providednot provided
3not applicablenot applicablenot providednot providednot providednot providednot providednot providednot provided

From Department of Pathology and Laboratory Medicine,Sinai Health System - The Canadian Open Genetics Repository (COGR), SCV001550285.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testingnot provided

Description

The PSAT1 p.Ile123Val variant was not identified in the literature nor was it identified in Cosmic or LOVD 3.0. The variant was identified in dbSNP (ID: rs116577685) and ClinVar (classified as likely benign by Illumina and as a VUS by Invitae). The variant was also identified in control databases in 180 of 282824 chromosomes (1 homozygous) at a frequency of 0.000636 increasing the likelihood this could be a low frequency benign variant (Genome Aggregation Database Feb 27, 2017). The variant was observed in the following populations: African in 166 of 24964 chromosomes (freq: 0.00665), Latino in 12 of 35434 chromosomes (freq: 0.000339), Other in 1 of 7224 chromosomes (freq: 0.000138) and European (non-Finnish) in 1 of 129142 chromosomes (freq: 0.000008), while the variant was not observed in the Ashkenazi Jewish, East Asian, European (Finnish), and South Asian populations. The p.Ile123 residue is not conserved in mammals and computational analyses (PolyPhen-2, SIFT, AlignGVGD, BLOSUM, MutationTaster) do not suggest a high likelihood of impact to the protein; however, this information is not predictive enough to rule out pathogenicity. The variant occurs outside of the splicing consensus sequence and in silico or computational prediction software programs (SpliceSiteFinder, MaxEntScan, NNSPLICE, GeneSplicer) do not predict a difference in splicing. In summary, based on the above information the clinical significance of this variant cannot be determined with certainty at this time although we would lean towards a more benign role for this variant. This variant is classified as likely benign.

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1unknownyesnot providednot providednot providednot providednot providednot providednot provided

Last Updated: May 23, 2021

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