NM_058179.4(PSAT1):c.367A>G (p.Ile123Val) AND Phosphoserine aminotransferase deficiency

Clinical significance:Likely benign (Last evaluated: Jan 12, 2018)

Review status:1 star out of maximum of 4 stars

criteria provided, single submitter

Based on:
1 submission [Details]
Record status:
current
Accession:
RCV000304704.2

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)

Name:
Phosphoserine aminotransferase deficiency (PSATD)
Synonyms:
PSAT DEFICIENCY
Identifiers:
MONDO: MONDO:0012596; MedGen: C1970253; Orphanet: 284417; OMIM: 610992

Recent activity

Your browsing activity is empty.

Activity recording is turned off.

Turn recording back on

See more...

Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV000480848Illumina Clinical Services Laboratory,Illuminacriteria provided, single submitter
Likely benign
(Jan 12, 2018)
germlineclinical testing

Citation Link

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineunknownnot providednot providednot providednot providednot providedclinical testing

Details of each submission

From Illumina Clinical Services Laboratory,Illumina, SCV000480848.3

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

Description

This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score and internal cut-off values, a variant classified as likely benign is not then subjected to further curation. The score for this variant resulted in a classification of likely benign for this disease.

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

Last Updated: May 23, 2021

Support Center