NM_058179.4(PSAT1):c.296C>T (p.Ala99Val) AND not provided

Germline classification:: Likely pathogenic (3 submissions)
Last evaluated:: Jul 18, 2023
Review status:: 2 stars out of maximum of 4 stars
criteria provided, multiple submitters, no conflicts

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:: RCV001254372.7

Allele description [Variation Report for NM_058179.4(PSAT1):c.296C>T (p.Ala99Val)]

NM_058179.4(PSAT1):c.296C>T (p.Ala99Val)

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.296C>T (p.Ala99Val)

HGVS:

NC_000009.12:g.78304839C>T
NG_012165.1:g.12697C>T
NM_021154.5:c.296C>T
NM_058179.4:c.296C>TMANE SELECT
NP_066977.1:p.Ala99Val
NP_478059.1:p.Ala99Val
NC_000009.11:g.80919755C>T
NM_058179.2:c.296C>T
NM_058179.3:c.296C>T
Q9Y617:p.Ala99Val

Protein change:

A99V; ALA99VAL

Links:

UniProtKB: Q9Y617#VAR_072571; OMIM: 610936.0004; dbSNP: rs587777778

NCBI 1000 Genomes Browser:

rs587777778

Molecular consequence:

NM_021154.5:c.296C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_058179.4:c.296C>T - missense variant - [Sequence Ontology: SO:0001583]

Functional consequence:

loss_of_function_variant [Sequence Ontology: SO:0002054] - Comment(s)
- Equally or more impaired than known disease allele D100A. PMID:32077105 Table S7.
mutation affecting polypeptide function [Sequence Ontology: SO:1000117] - Comment(s)
- More impaired than known disease allele D100A. PMID:32077105 Table S7.

Condition(s)

Synonyms:: none provided
Identifiers:: MedGen: C3661900

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV001430349	Dudley Research Group, Pacific Northwest Research Institute	no classification provided	not provided	unknown, not applicable	research, in vivo	PubMed (1) [See all records that cite this PMID]
SCV002064403	Genetic Services Laboratory, University of Chicago	criteria provided, single submitter (ACMG Guidelines, 2015)	Likely pathogenic (Jun 20, 2017)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]
SCV004238604	Revvity Omics, Revvity	criteria provided, single submitter (ACMG Guidelines, 2015)	Likely pathogenic (Jul 18, 2023)	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

SCV001430349

Dudley Research Group, Pacific Northwest Research Institute

no classification provided

not provided

unknown, not applicable

research, in vivo

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

SCV002064403

Genetic Services Laboratory, University of Chicago

criteria provided, single submitter

(ACMG Guidelines, 2015)

Likely pathogenic
(Jun 20, 2017)

germline

clinical testing

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

SCV004238604

Revvity Omics, Revvity

criteria provided, single submitter

(ACMG Guidelines, 2015)

Likely pathogenic
(Jul 18, 2023)

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	not applicable	not applicable	not provided	not provided	not provided	not provided	not provided	in vivo
not provided	unknown	unknown	not provided	not provided	not provided	not provided	not provided	research
not provided	germline	yes	not provided	not provided	not provided	not provided	not provided	clinical testing
not provided	germline	unknown	not provided	not provided	not provided	not provided	not provided	clinical testing

Citations

PubMed

Nothing to display

Details of each submission

From Dudley Research Group, Pacific Northwest Research Institute, SCV001430349.2

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	research	PubMed (1)
2	not provided	not provided	not provided	not provided	in vivo	PubMed (1)
3	not provided	not provided	not provided	not provided	in vivo	PubMed (1)

Description

"Equally or more impaired in assay than known disease alleles D100A and A99V."

PubMed [ID: 32077105]

"Equally or more impaired in assay than known disease allele D100A."

PubMed [ID: 32077105]

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

From Genetic Services Laboratory, University of Chicago, SCV002064403.1

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

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

From Revvity Omics, Revvity, SCV004238604.1

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

#	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: Mar 16, 2024

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