NM_004577.4(PSPH):c.379G>A (p.Ala127Thr) 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:: May 22, 2023
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:: RCV002976050.2

Allele description

NM_004577.4(PSPH):c.379G>A (p.Ala127Thr)

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.379G>A (p.Ala127Thr)

HGVS:

NC_000007.14:g.56017276C>T
NG_011473.1:g.39300G>A
NM_001370503.1:c.379G>A
NM_001370504.1:c.379G>A
NM_001370505.1:c.379G>A
NM_001370506.1:c.379G>A
NM_001370507.1:c.379G>A
NM_001370508.1:c.379G>A
NM_001370509.1:c.379G>A
NM_001370510.1:c.379G>A
NM_001370511.1:c.379G>A
NM_001370512.1:c.379G>A
NM_001370513.1:c.379G>A
NM_001370514.1:c.379G>A
NM_001370515.1:c.379G>A
NM_001370516.1:c.379G>A
NM_001370517.1:c.379G>A
NM_001370518.1:c.379G>A
NM_001370519.1:c.379G>A
NM_001370520.1:c.379G>A
NM_001370521.1:c.379G>A
NM_001370522.1:c.379G>A
NM_004577.4:c.379G>AMANE SELECT
NP_001357432.1:p.Ala127Thr
NP_001357433.1:p.Ala127Thr
NP_001357434.1:p.Ala127Thr
NP_001357435.1:p.Ala127Thr
NP_001357436.1:p.Ala127Thr
NP_001357437.1:p.Ala127Thr
NP_001357438.1:p.Ala127Thr
NP_001357439.1:p.Ala127Thr
NP_001357440.1:p.Ala127Thr
NP_001357441.1:p.Ala127Thr
NP_001357442.1:p.Ala127Thr
NP_001357443.1:p.Ala127Thr
NP_001357444.1:p.Ala127Thr
NP_001357445.1:p.Ala127Thr
NP_001357446.1:p.Ala127Thr
NP_001357447.1:p.Ala127Thr
NP_001357448.1:p.Ala127Thr
NP_001357449.1:p.Ala127Thr
NP_001357450.1:p.Ala127Thr
NP_001357451.1:p.Ala127Thr
NP_004568.2:p.Ala127Thr
NC_000007.13:g.56084969C>T

Protein change:

A127T

Molecular consequence:

NM_001370503.1:c.379G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001370504.1:c.379G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001370505.1:c.379G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001370506.1:c.379G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001370507.1:c.379G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001370508.1:c.379G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001370509.1:c.379G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001370510.1:c.379G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001370511.1:c.379G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001370512.1:c.379G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001370513.1:c.379G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001370514.1:c.379G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001370515.1:c.379G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001370516.1:c.379G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001370517.1:c.379G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001370518.1:c.379G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001370519.1:c.379G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001370520.1:c.379G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001370521.1:c.379G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001370522.1:c.379G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_004577.4:c.379G>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

Recent activity

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regulator of nonsense transcripts 3A isoform X2 [Homo sapiens]
regulator of nonsense transcripts 3A isoform X2 [Homo sapiens]
gi|767979384|ref|XP_011533147.1|

Protein
PREDICTED: Homo sapiens UPF3A regulator of nonsense mediated mRNA decay (UPF3A),...
PREDICTED: Homo sapiens UPF3A regulator of nonsense mediated mRNA decay (UPF3A), transcript variant X3, mRNA
gi|2462537770|ref|XM_054374868.1|

Nucleotide

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV003287403	Invitae	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (May 22, 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

SCV003287403

Invitae

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(May 22, 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	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, SCV003287403.2

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

Description

This sequence change replaces alanine, which is neutral and non-polar, with threonine, which is neutral and polar, at codon 127 of the PSPH protein (p.Ala127Thr). This variant is present in population databases (rs768449967, gnomAD 0.006%). This variant has not been reported in the literature in individuals affected with PSPH-related conditions. ClinVar contains an entry for this variant (Variation ID: 2074117). Algorithms developed to predict the effect of missense changes on protein structure and function output the following: SIFT: "Not Available"; PolyPhen-2: "Benign"; Align-GVGD: "Not Available". The threonine amino acid residue is found in multiple mammalian species, which suggests that this missense change does not adversely affect protein function. 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 28, 2024

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