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NM_058179.4(PSAT1):c.107del (p.Gly36fs)

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Interpretation:
Pathogenic​

Review status:
no assertion criteria provided
Submissions:
2 (Most recent: Mar 12, 2021)
Last evaluated:
May 1, 2007
Accession:
VCV000001081.4
Variation ID:
1081
Description:
1bp deletion
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NM_058179.4(PSAT1):c.107del (p.Gly36fs)

Allele ID
16120
Variant type
Deletion
Variant length
1 bp
Cytogenetic location
9q21.2
Genomic location
9: 78300647 (GRCh38) GRCh38 UCSC
9: 80915563 (GRCh37) GRCh37 UCSC
HGVS
Nucleotide Protein Molecular
consequence
NC_000009.11:g.80915564del
NC_000009.12:g.78300648del
NM_058179.4:c.107del MANE Select NP_478059.1:p.Gly36fs frameshift
... more HGVS
Protein change
G36fs
Other names
-
Canonical SPDI
NC_000009.12:78300646:GG:G
Functional consequence
mutation affecting polypeptide function [Sequence Ontology SO:1000117]
More impaired than known disease alleles D100A and A99V. PMID:32077105 Table S7. [submitted by Dudley Research Group,Pacific Northwest Research Institute]
mutation affecting reading frame [Sequence Ontology SO:1000064]
loss_of_function_variant [Sequence Ontology SO:0002054]
Equally or more impaired than known disease alleles D100A and A99V. PMID:32077105 Table S7. [submitted by Dudley Research Group,Pacific Northwest Research Institute]
Global minor allele frequency (GMAF)
-

Allele frequency
-
Links
ClinGen: CA114738
OMIM: 610936.0001
dbSNP: rs587777747
VarSome
Comment on variant
NCBI staff reviewed the sequence information reported in PubMed 17436247 Fig. 2 to determine the location of this allele on the current reference sequence.
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Aggregate interpretations per condition

Interpreted condition Interpretation Number of submissions Review status Last evaluated Variation/condition record
Pathogenic 1 no assertion criteria provided May 1, 2007 RCV000001136.5
not provided 1 no assertion provided - RCV001254415.1
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Gene OMIM ClinGen Gene Dosage Sensitivity Curation Variation viewer Related variants
HI score Help TS score Help Within gene All
PSAT1 - - GRCh38
GRCh37
314 354

Submitted interpretations and evidence

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Interpretation
(Last evaluated)
Review status
(Assertion criteria)
Condition
(Inheritance)
Submitter Supporting information
Pathogenic
(May 01, 2007)
no assertion criteria provided
Method: literature only
PHOSPHOSERINE AMINOTRANSFERASE DEFICIENCY
Allele origin: germline
OMIM
Accession: SCV000021286.4
Submitted: (Dec 30, 2010)
Evidence details
Publications
PubMed (1)
not provided
(-)
no assertion provided
Method: research, in vivo
not provided
Allele origin: unknown, not applicable
Dudley Research Group,Pacific Northwest Research Institute
Accession: SCV001430392.2
Submitted: (Mar 12, 2021)
Evidence details
Publications
PubMed (1)

Functional evidence

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Functional consequence Method Result Submitter Supporting information
loss_of_function_variant
  1. Method not provided
  2. Relative growth in yeast complementation assay. Null and wt values set to 0% and 100%, respectively.
  3. Method citation(s):
  1. Result not provided
  2. -1.175% +/- 1.857 (SE)
Dudley Research Group,Pacific Northwest Research Institute
Accession: SCV001430392.2
Submitted: (Mar 12, 2021)
Evidence details
Publications
PubMed (1)
Comment:
Equally or more impaired than known disease alleles D100A and A99V. PMID:32077105 Table S7.

Citations for this variant

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Title Author Journal Year Link
A yeast-based complementation assay elucidates the functional impact of 200 missense variants in human PSAT1. Sirr A Journal of inherited metabolic disease 2020 PMID: 32077105
Phosphoserine aminotransferase deficiency: a novel disorder of the serine biosynthesis pathway. Hart CE American journal of human genetics 2007 PMID: 17436247

Text-mined citations for rs587777747...

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These citations are identified by LitVar using the rs number, so they may include citations for more than one variant at this location. Please review the LitVar results carefully for your variant of interest.

Record last updated Mar 22, 2021