NM_004577.4(PSPH):c.-3G>A AND Deficiency of phosphoserine phosphatase

Germline classification:: Likely benign (1 submission)
Last evaluated:: May 12, 2021
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:: RCV001391295.2

Allele description [Variation Report for NM_004577.4(PSPH):c.-3G>A]

NM_004577.4(PSPH):c.-3G>A

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.-3G>A

HGVS:

NC_000007.14:g.56021215C>T
NG_011473.1:g.35361G>A
NM_001370503.1:c.-3G>A
NM_001370504.1:c.-3G>A
NM_001370505.1:c.-3G>A
NM_001370506.1:c.-3G>A
NM_001370507.1:c.-3G>A
NM_001370508.1:c.-3G>A
NM_001370509.1:c.-3G>A
NM_001370510.1:c.-3G>A
NM_001370511.1:c.-3G>A
NM_001370512.1:c.-3G>A
NM_001370513.1:c.-3G>A
NM_001370514.1:c.-3G>A
NM_001370515.1:c.-3G>A
NM_001370516.1:c.-3G>A
NM_001370517.1:c.-3G>A
NM_001370518.1:c.-3G>A
NM_001370519.1:c.-3G>A
NM_001370520.1:c.-3G>A
NM_001370521.1:c.-3G>A
NM_001370522.1:c.-3G>A
NM_004577.4:c.-3G>AMANE SELECT
NC_000007.13:g.56088908C>T

Links:

dbSNP: rs201958642

NCBI 1000 Genomes Browser:

rs201958642

Molecular consequence:

NM_001370503.1:c.-3G>A - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001370504.1:c.-3G>A - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001370505.1:c.-3G>A - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001370506.1:c.-3G>A - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001370507.1:c.-3G>A - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001370508.1:c.-3G>A - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001370509.1:c.-3G>A - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001370510.1:c.-3G>A - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001370511.1:c.-3G>A - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001370512.1:c.-3G>A - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001370513.1:c.-3G>A - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001370514.1:c.-3G>A - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001370515.1:c.-3G>A - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001370516.1:c.-3G>A - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001370517.1:c.-3G>A - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001370518.1:c.-3G>A - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001370519.1:c.-3G>A - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001370520.1:c.-3G>A - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001370521.1:c.-3G>A - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001370522.1:c.-3G>A - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_004577.4:c.-3G>A - 5 prime UTR variant - [Sequence Ontology: SO:0001623]

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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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV001593266	Genome-Nilou Lab	criteria provided, single submitter (ACMG Guidelines, 2015)	Likely benign (May 12, 2021)	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

SCV001593266

Genome-Nilou Lab

criteria provided, single submitter

(ACMG Guidelines, 2015)

Likely benign
(May 12, 2021)

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	germline	no	not provided	not provided	not provided	not provided	not provided	clinical testing

Citations

PubMed

Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology.

Richards S, Aziz N, Bale S, Bick D, Das S, Gastier-Foster J, Grody WW, Hegde M, Lyon E, Spector E, Voelkerding K, Rehm HL; ACMG Laboratory Quality Assurance Committee..

Genet Med. 2015 May;17(5):405-24. doi: 10.1038/gim.2015.30. Epub 2015 Mar 5.

PubMed [citation]

PMID:: 25741868
PMCID:: PMC4544753

Details of each submission

From Genome-Nilou Lab, SCV001593266.1

#	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	no	not provided	not provided	not provided		not provided	not provided	not provided	not provided

Last Updated: Sep 29, 2024

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