NM_004577.4(PSPH):c.593G>A (p.Gly198Glu) AND Deficiency of phosphoserine phosphatase

This record was updated by the submitter. Please see the current version.

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Jul 10, 2022
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:: RCV002843567.2

Allele description

NM_004577.4(PSPH):c.593G>A (p.Gly198Glu)

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.593G>A (p.Gly198Glu)

HGVS:

NC_000007.14:g.56011847C>T
NG_011473.1:g.44729G>A
NM_001370503.1:c.593G>A
NM_001370504.1:c.593G>A
NM_001370505.1:c.593G>A
NM_001370506.1:c.593G>A
NM_001370507.1:c.593G>A
NM_001370508.1:c.593G>A
NM_001370509.1:c.593G>A
NM_001370510.1:c.593G>A
NM_001370511.1:c.593G>A
NM_001370512.1:c.593G>A
NM_001370513.1:c.593G>A
NM_001370514.1:c.593G>A
NM_001370515.1:c.593G>A
NM_001370516.1:c.593G>A
NM_001370517.1:c.593G>A
NM_001370518.1:c.593G>A
NM_001370519.1:c.593G>A
NM_001370520.1:c.593G>A
NM_001370521.1:c.593G>A
NM_001370522.1:c.593G>A
NM_004577.4:c.593G>AMANE SELECT
NP_001357432.1:p.Gly198Glu
NP_001357433.1:p.Gly198Glu
NP_001357434.1:p.Gly198Glu
NP_001357435.1:p.Gly198Glu
NP_001357436.1:p.Gly198Glu
NP_001357437.1:p.Gly198Glu
NP_001357438.1:p.Gly198Glu
NP_001357439.1:p.Gly198Glu
NP_001357440.1:p.Gly198Glu
NP_001357441.1:p.Gly198Glu
NP_001357442.1:p.Gly198Glu
NP_001357443.1:p.Gly198Glu
NP_001357444.1:p.Gly198Glu
NP_001357445.1:p.Gly198Glu
NP_001357446.1:p.Gly198Glu
NP_001357447.1:p.Gly198Glu
NP_001357448.1:p.Gly198Glu
NP_001357449.1:p.Gly198Glu
NP_001357450.1:p.Gly198Glu
NP_001357451.1:p.Gly198Glu
NP_004568.2:p.Gly198Glu
NC_000007.13:g.56079540C>T

Protein change:

G198E

Molecular consequence:

NM_001370503.1:c.593G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001370504.1:c.593G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001370505.1:c.593G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001370506.1:c.593G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001370507.1:c.593G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001370508.1:c.593G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001370509.1:c.593G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001370510.1:c.593G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001370511.1:c.593G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001370512.1:c.593G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001370513.1:c.593G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001370514.1:c.593G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001370515.1:c.593G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001370516.1:c.593G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001370517.1:c.593G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001370518.1:c.593G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001370519.1:c.593G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001370520.1:c.593G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001370521.1:c.593G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001370522.1:c.593G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_004577.4:c.593G>A - missense variant - [Sequence Ontology: SO:0001583]

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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BLTP1 bridge-like lipid transfer protein family member 1 [Homo sapiens]
BLTP1 bridge-like lipid transfer protein family member 1 [Homo sapiens]
Gene ID:84162

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV003220290	Invitae	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (Jul 10, 2022)	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

SCV003220290

Invitae

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(Jul 10, 2022)

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	unknown	not provided	not provided	not provided	not provided	not provided	clinical testing

Citations

PubMed

Sherloc: a comprehensive refinement of the ACMG-AMP variant classification criteria.

Nykamp K, Anderson M, Powers M, Garcia J, Herrera B, Ho YY, Kobayashi Y, Patil N, Thusberg J, Westbrook M; Invitae Clinical Genomics Group., Topper S.

Genet Med. 2017 Oct;19(10):1105-1117. doi: 10.1038/gim.2017.37. Epub 2017 May 11. Erratum in: Genet Med. 2020 Jan;22(1):240. doi: 10.1038/s41436-019-0624-9.

PubMed [citation]

PMID:: 28492532
PMCID:: PMC5632818

Details of each submission

From Invitae, SCV003220290.2

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

Description

This variant has not been reported in the literature in individuals affected with PSPH-related conditions. This variant is not present in population databases (gnomAD no frequency). This sequence change replaces glycine, which is neutral and non-polar, with glutamic acid, which is acidic and polar, at codon 198 of the PSPH protein (p.Gly198Glu). Algorithms developed to predict the effect of missense changes on protein structure and function are either unavailable or do not agree on the potential impact of this missense change (SIFT: "Deleterious"; PolyPhen-2: "Probably Damaging"; Align-GVGD: "Class C15"). In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance.

#	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: Feb 20, 2024

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