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NM_004577.4(PSPH):c.*8T>C AND Deficiency of phosphoserine phosphatase

Germline classification:
Benign (1 submission)
Last evaluated:
Apr 27, 2017
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:
RCV001161985.4

Allele description [Variation Report for NM_004577.4(PSPH):c.*8T>C]

NM_004577.4(PSPH):c.*8T>C

Gene:
PSPH:phosphoserine phosphatase [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
7p11.2
Genomic location:
Preferred name:
NM_004577.4(PSPH):c.*8T>C
HGVS:
  • NC_000007.14:g.56011754A>G
  • NG_011473.1:g.44822T>C
  • NM_001370503.1:c.*8T>C
  • NM_001370504.1:c.*8T>C
  • NM_001370505.1:c.*8T>C
  • NM_001370506.1:c.*8T>C
  • NM_001370507.1:c.*8T>C
  • NM_001370508.1:c.*8T>C
  • NM_001370509.1:c.*8T>C
  • NM_001370510.1:c.*8T>C
  • NM_001370511.1:c.*8T>C
  • NM_001370512.1:c.*8T>C
  • NM_001370513.1:c.*8T>C
  • NM_001370514.1:c.*8T>C
  • NM_001370515.1:c.*8T>C
  • NM_001370516.1:c.*8T>C
  • NM_001370517.1:c.*8T>C
  • NM_001370518.1:c.*8T>C
  • NM_001370519.1:c.*8T>C
  • NM_001370520.1:c.*8T>C
  • NM_001370521.1:c.*8T>C
  • NM_001370522.1:c.*8T>C
  • NM_004577.4:c.*8T>CMANE SELECT
  • NC_000007.13:g.56079447A>G
  • NM_004577.3:c.*8T>C
Links:
dbSNP: rs140998795
NCBI 1000 Genomes Browser:
rs140998795
Molecular consequence:
  • NM_001370503.1:c.*8T>C - 3 prime UTR variant - [Sequence Ontology: SO:0001624]
  • NM_001370504.1:c.*8T>C - 3 prime UTR variant - [Sequence Ontology: SO:0001624]
  • NM_001370505.1:c.*8T>C - 3 prime UTR variant - [Sequence Ontology: SO:0001624]
  • NM_001370506.1:c.*8T>C - 3 prime UTR variant - [Sequence Ontology: SO:0001624]
  • NM_001370507.1:c.*8T>C - 3 prime UTR variant - [Sequence Ontology: SO:0001624]
  • NM_001370508.1:c.*8T>C - 3 prime UTR variant - [Sequence Ontology: SO:0001624]
  • NM_001370509.1:c.*8T>C - 3 prime UTR variant - [Sequence Ontology: SO:0001624]
  • NM_001370510.1:c.*8T>C - 3 prime UTR variant - [Sequence Ontology: SO:0001624]
  • NM_001370511.1:c.*8T>C - 3 prime UTR variant - [Sequence Ontology: SO:0001624]
  • NM_001370512.1:c.*8T>C - 3 prime UTR variant - [Sequence Ontology: SO:0001624]
  • NM_001370513.1:c.*8T>C - 3 prime UTR variant - [Sequence Ontology: SO:0001624]
  • NM_001370514.1:c.*8T>C - 3 prime UTR variant - [Sequence Ontology: SO:0001624]
  • NM_001370515.1:c.*8T>C - 3 prime UTR variant - [Sequence Ontology: SO:0001624]
  • NM_001370516.1:c.*8T>C - 3 prime UTR variant - [Sequence Ontology: SO:0001624]
  • NM_001370517.1:c.*8T>C - 3 prime UTR variant - [Sequence Ontology: SO:0001624]
  • NM_001370518.1:c.*8T>C - 3 prime UTR variant - [Sequence Ontology: SO:0001624]
  • NM_001370519.1:c.*8T>C - 3 prime UTR variant - [Sequence Ontology: SO:0001624]
  • NM_001370520.1:c.*8T>C - 3 prime UTR variant - [Sequence Ontology: SO:0001624]
  • NM_001370521.1:c.*8T>C - 3 prime UTR variant - [Sequence Ontology: SO:0001624]
  • NM_001370522.1:c.*8T>C - 3 prime UTR variant - [Sequence Ontology: SO:0001624]
  • NM_004577.4:c.*8T>C - 3 prime UTR variant - [Sequence Ontology: SO:0001624]

Condition(s)

Name:
Deficiency of phosphoserine phosphatase (PSPHD)
Synonyms:
Phosphoserine phosphatase deficiency; PSPH deficiency
Identifiers:
MONDO: MONDO:0013531; MedGen: C1291463; OMIM: 614023

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Assertion and evidence details

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Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV001323911Illumina Laboratory Services, Illumina
criteria provided, single submitter

(ICSL Variant Classification Criteria 13 December 2019)		Benign
(Apr 27, 2017) 		germlineclinical testing

Citation Link

Help

Summary from all submissions

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

Details of each submission

From Illumina Laboratory Services, Illumina, SCV001323911.1

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

Description

This variant was observed as part of a predisposition screen in an ostensibly healthy population. A literature search was performed for the gene, cDNA change, and amino acid change (where applicable). No publications were found based on this search. Allele frequency data from public databases was too high to be consistent with this variant causing disease. Therefore, this variant is classified as benign.

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

Last Updated: Dec 24, 2023