NM_004577.4(PSPH):c.316T>C (p.Phe106Leu) 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 19, 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:: RCV001928483.4

Allele description

NM_004577.4(PSPH):c.316T>C (p.Phe106Leu)

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.316T>C (p.Phe106Leu)

HGVS:

NC_000007.14:g.56017339A>G
NG_011473.1:g.39237T>C
NM_001370503.1:c.316T>C
NM_001370504.1:c.316T>C
NM_001370505.1:c.316T>C
NM_001370506.1:c.316T>C
NM_001370507.1:c.316T>C
NM_001370508.1:c.316T>C
NM_001370509.1:c.316T>C
NM_001370510.1:c.316T>C
NM_001370511.1:c.316T>C
NM_001370512.1:c.316T>C
NM_001370513.1:c.316T>C
NM_001370514.1:c.316T>C
NM_001370515.1:c.316T>C
NM_001370516.1:c.316T>C
NM_001370517.1:c.316T>C
NM_001370518.1:c.316T>C
NM_001370519.1:c.316T>C
NM_001370520.1:c.316T>C
NM_001370521.1:c.316T>C
NM_001370522.1:c.316T>C
NM_004577.4:c.316T>CMANE SELECT
NP_001357432.1:p.Phe106Leu
NP_001357433.1:p.Phe106Leu
NP_001357434.1:p.Phe106Leu
NP_001357435.1:p.Phe106Leu
NP_001357436.1:p.Phe106Leu
NP_001357437.1:p.Phe106Leu
NP_001357438.1:p.Phe106Leu
NP_001357439.1:p.Phe106Leu
NP_001357440.1:p.Phe106Leu
NP_001357441.1:p.Phe106Leu
NP_001357442.1:p.Phe106Leu
NP_001357443.1:p.Phe106Leu
NP_001357444.1:p.Phe106Leu
NP_001357445.1:p.Phe106Leu
NP_001357446.1:p.Phe106Leu
NP_001357447.1:p.Phe106Leu
NP_001357448.1:p.Phe106Leu
NP_001357449.1:p.Phe106Leu
NP_001357450.1:p.Phe106Leu
NP_001357451.1:p.Phe106Leu
NP_004568.2:p.Phe106Leu
NC_000007.13:g.56085032A>G

Protein change:

F106L

Links:

dbSNP: rs1295914487

NCBI 1000 Genomes Browser:

rs1295914487

Molecular consequence:

NM_001370503.1:c.316T>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001370504.1:c.316T>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001370505.1:c.316T>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001370506.1:c.316T>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001370507.1:c.316T>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001370508.1:c.316T>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001370509.1:c.316T>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001370510.1:c.316T>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001370511.1:c.316T>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001370512.1:c.316T>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001370513.1:c.316T>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001370514.1:c.316T>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001370515.1:c.316T>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001370516.1:c.316T>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001370517.1:c.316T>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001370518.1:c.316T>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001370519.1:c.316T>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001370520.1:c.316T>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001370521.1:c.316T>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001370522.1:c.316T>C - missense variant - [Sequence Ontology: SO:0001583]
NM_004577.4:c.316T>C - 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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zinc finger protein 573 isoform 4 [Homo sapiens]
zinc finger protein 573 isoform 4 [Homo sapiens]
gi|289577063|ref|NP_001166162.1|

Protein
PREDICTED: Homo sapiens nucleosome assembly protein 1 like 1 (NAP1L1), transcrip...
PREDICTED: Homo sapiens nucleosome assembly protein 1 like 1 (NAP1L1), transcript variant X4, mRNA
gi|2217289171|ref|XM_047428879.1|

Nucleotide

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV002183734	Invitae	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (Jul 19, 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

SCV002183734

Invitae

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(Jul 19, 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, SCV002183734.2

#	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 phenylalanine, which is neutral and non-polar, with leucine, which is neutral and non-polar, at codon 106 of the PSPH protein (p.Phe106Leu). This variant is present in population databases (no rsID available, gnomAD 0.0009%). 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: 1414019). 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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