NM_004577.4(PSPH):c.94G>A (p.Asp32Asn) AND Deficiency of phosphoserine phosphatase

Germline classification:: Uncertain significance (2 submissions)
Last evaluated:: May 11, 2018
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:: RCV000014593.28

Allele description [Variation Report for NM_004577.4(PSPH):c.94G>A (p.Asp32Asn)]

NM_004577.4(PSPH):c.94G>A (p.Asp32Asn)

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.94G>A (p.Asp32Asn)

HGVS:

NC_000007.14:g.56021119C>T
NG_011473.1:g.35457G>A
NM_001370503.1:c.94G>A
NM_001370504.1:c.94G>A
NM_001370505.1:c.94G>A
NM_001370506.1:c.94G>A
NM_001370507.1:c.94G>A
NM_001370508.1:c.94G>A
NM_001370509.1:c.94G>A
NM_001370510.1:c.94G>A
NM_001370511.1:c.94G>A
NM_001370512.1:c.94G>A
NM_001370513.1:c.94G>A
NM_001370514.1:c.94G>A
NM_001370515.1:c.94G>A
NM_001370516.1:c.94G>A
NM_001370517.1:c.94G>A
NM_001370518.1:c.94G>A
NM_001370519.1:c.94G>A
NM_001370520.1:c.94G>A
NM_001370521.1:c.94G>A
NM_001370522.1:c.94G>A
NM_004577.4:c.94G>AMANE SELECT
NP_001357432.1:p.Asp32Asn
NP_001357433.1:p.Asp32Asn
NP_001357434.1:p.Asp32Asn
NP_001357435.1:p.Asp32Asn
NP_001357436.1:p.Asp32Asn
NP_001357437.1:p.Asp32Asn
NP_001357438.1:p.Asp32Asn
NP_001357439.1:p.Asp32Asn
NP_001357440.1:p.Asp32Asn
NP_001357441.1:p.Asp32Asn
NP_001357442.1:p.Asp32Asn
NP_001357443.1:p.Asp32Asn
NP_001357444.1:p.Asp32Asn
NP_001357445.1:p.Asp32Asn
NP_001357446.1:p.Asp32Asn
NP_001357447.1:p.Asp32Asn
NP_001357448.1:p.Asp32Asn
NP_001357449.1:p.Asp32Asn
NP_001357450.1:p.Asp32Asn
NP_001357451.1:p.Asp32Asn
NP_004568.2:p.Asp32Asn
NC_000007.13:g.56088812C>T
NM_004577.3:c.94G>A
P78330:p.Asp32Asn

Protein change:

D32N; ASP32ASN

Links:

UniProtKB: P78330#VAR_022378; OMIM: 172480.0001; dbSNP: rs104894035

NCBI 1000 Genomes Browser:

rs104894035

Molecular consequence:

NM_001370503.1:c.94G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001370504.1:c.94G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001370505.1:c.94G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001370506.1:c.94G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001370507.1:c.94G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001370508.1:c.94G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001370509.1:c.94G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001370510.1:c.94G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001370511.1:c.94G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001370512.1:c.94G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001370513.1:c.94G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001370514.1:c.94G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001370515.1:c.94G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001370516.1:c.94G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001370517.1:c.94G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001370518.1:c.94G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001370519.1:c.94G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001370520.1:c.94G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001370521.1:c.94G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001370522.1:c.94G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_004577.4:c.94G>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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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000034847	OMIM	no assertion criteria provided	Pathogenic (Feb 1, 2004)	germline	literature only	PubMed (2) [See all records that cite these PMIDs] 9222972, 14673469
SCV001528239	Baylor Genetics	criteria provided, single submitter (ACMG Guidelines, 2015)	Uncertain significance (May 11, 2018)	unknown	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

SCV000034847

OMIM

no assertion criteria provided

Pathogenic
(Feb 1, 2004)

germline

literature only

PubMed (2)
[See all records that cite these PMIDs]

SCV001528239

Baylor Genetics

criteria provided, single submitter

(ACMG Guidelines, 2015)

Uncertain significance
(May 11, 2018)

unknown

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	unknown	yes	not provided	not provided	not provided	not provided	not provided	clinical testing
not provided	germline	not provided	not provided	not provided	not provided	not provided	not provided	literature only

Citations

PubMed

Phosphoserine phosphatase deficiency in a patient with Williams syndrome.

Jaeken J, Detheux M, Fryns JP, Collet JF, Alliet P, Van Schaftingen E.

J Med Genet. 1997 Jul;34(7):594-6.

PubMed [citation]

PMID:: 9222972
PMCID:: PMC1051004

Mutations responsible for 3-phosphoserine phosphatase deficiency.

Veiga-da-Cunha M, Collet JF, Prieur B, Jaeken J, Peeraer Y, Rabbijns A, Van Schaftingen E.

Eur J Hum Genet. 2004 Feb;12(2):163-6.

PubMed [citation]

PMID:: 14673469

See all PubMed Citations (3)

Details of each submission

From OMIM, SCV000034847.4

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	literature only	PubMed (2)

Description

In a patient with phosphoserine phosphatase deficiency (PSPHD; 614023) originally reported by Jaeken et al. (1997), Veiga-da-Cunha et al. (2004) identified compound heterozygosity for 2 mutations in the PSPH gene: a 94G-A transition resulting in an asp32-to-asn (D32N) substitution, and a 155T-C transition resulting in a met52-to-thr (M52T; 172480.0002) substitution. The D32N change occurs in a fairly well-conserved region of the protein, and the M52T change in an extremely well-conserved area. The patient's father and mother were heterozygous for the D32N and the M52T mutation, respectively, indicating autosomal recessive inheritance. In vitro expression studies showed that the D32N mutation reduced enzyme activity by 50%, and the M52T mutation virtually abolished enzyme activity. The changes were consistent with kinetic properties observed in the patient's fibroblasts.

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	not provided	not provided	not provided	not provided		not provided	not provided	not provided	not provided

From Baylor Genetics, SCV001528239.1

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

Description

This variant was determined to be of uncertain significance according to ACMG Guidelines, 2015 [PMID:25741868].

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	unknown	yes	not provided	not provided	not provided		not provided	not provided	not provided	not provided

Last Updated: Aug 25, 2024

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