NM_004577.4(PSPH):c.386A>G (p.Asn129Ser) 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:: Jun 20, 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:: RCV001981160.2

Allele description

NM_004577.4(PSPH):c.386A>G (p.Asn129Ser)

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.386A>G (p.Asn129Ser)

HGVS:

NC_000007.14:g.56017269T>C
NG_011473.1:g.39307A>G
NM_001370503.1:c.386A>G
NM_001370504.1:c.386A>G
NM_001370505.1:c.386A>G
NM_001370506.1:c.386A>G
NM_001370507.1:c.386A>G
NM_001370508.1:c.386A>G
NM_001370509.1:c.386A>G
NM_001370510.1:c.386A>G
NM_001370511.1:c.386A>G
NM_001370512.1:c.386A>G
NM_001370513.1:c.386A>G
NM_001370514.1:c.386A>G
NM_001370515.1:c.386A>G
NM_001370516.1:c.386A>G
NM_001370517.1:c.386A>G
NM_001370518.1:c.386A>G
NM_001370519.1:c.386A>G
NM_001370520.1:c.386A>G
NM_001370521.1:c.386A>G
NM_001370522.1:c.386A>G
NM_004577.4:c.386A>GMANE SELECT
NP_001357432.1:p.Asn129Ser
NP_001357433.1:p.Asn129Ser
NP_001357434.1:p.Asn129Ser
NP_001357435.1:p.Asn129Ser
NP_001357436.1:p.Asn129Ser
NP_001357437.1:p.Asn129Ser
NP_001357438.1:p.Asn129Ser
NP_001357439.1:p.Asn129Ser
NP_001357440.1:p.Asn129Ser
NP_001357441.1:p.Asn129Ser
NP_001357442.1:p.Asn129Ser
NP_001357443.1:p.Asn129Ser
NP_001357444.1:p.Asn129Ser
NP_001357445.1:p.Asn129Ser
NP_001357446.1:p.Asn129Ser
NP_001357447.1:p.Asn129Ser
NP_001357448.1:p.Asn129Ser
NP_001357449.1:p.Asn129Ser
NP_001357450.1:p.Asn129Ser
NP_001357451.1:p.Asn129Ser
NP_004568.2:p.Asn129Ser
NC_000007.13:g.56084962T>C

Protein change:

N129S

Links:

dbSNP: rs771251320

NCBI 1000 Genomes Browser:

rs771251320

Molecular consequence:

NM_001370503.1:c.386A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001370504.1:c.386A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001370505.1:c.386A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001370506.1:c.386A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001370507.1:c.386A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001370508.1:c.386A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001370509.1:c.386A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001370510.1:c.386A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001370511.1:c.386A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001370512.1:c.386A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001370513.1:c.386A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001370514.1:c.386A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001370515.1:c.386A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001370516.1:c.386A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001370517.1:c.386A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001370518.1:c.386A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001370519.1:c.386A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001370520.1:c.386A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001370521.1:c.386A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001370522.1:c.386A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_004577.4:c.386A>G - 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

Clear Turn Off Turn On

LysR family transcriptional regulator [Serratia marcescens]
LysR family transcriptional regulator [Serratia marcescens]
gi|2734167862|ref|WP_346411885.1|

Protein
Homo sapiens zinc finger DHHC-type palmitoyltransferase 6 (ZDHHC6), transcript v...
Homo sapiens zinc finger DHHC-type palmitoyltransferase 6 (ZDHHC6), transcript variant 1, mRNA
gi|1519246150|ref|NM_022494.3|

Nucleotide
CBTC1279.rev NICHD_XGC_tropBone1 Xenopus tropicalis cDNA clone IMAGE:8933769 3',...
CBTC1279.rev NICHD_XGC_tropBone1 Xenopus tropicalis cDNA clone IMAGE:8933769 3', mRNA sequence
gi|126261390|gnl|dbEST|45035054|gb| 502.1|

Nucleotide

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV002283397	Invitae	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (Jun 20, 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

SCV002283397

Invitae

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(Jun 20, 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, SCV002283397.2

#	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 asparagine, which is neutral and polar, with serine, which is neutral and polar, at codon 129 of the PSPH protein (p.Asn129Ser). This variant is present in population databases (rs771251320, gnomAD 0.007%). This variant has not been reported in the literature in individuals affected with PSPH-related conditions. 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: "Tolerated"; PolyPhen-2: "Possibly Damaging"; Align-GVGD: "Class C0"). 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: Dec 24, 2023

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