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NC_000007.13:g.(?_56079455)_(56085092_?)dup AND Deficiency of phosphoserine phosphatase

Germline classification:
Uncertain significance (1 submission)
Last evaluated:
Sep 27, 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:
RCV001953128.4

Allele description

NC_000007.13:g.(?_56079455)_(56085092_?)dup

Gene:
PSPH:phosphoserine phosphatase [Gene - OMIM - HGNC]
Variant type:
Duplication
Cytogenetic location:
7p11.2
Genomic location:
Chr7: 56079455 - 56085092 (on Assembly GRCh37)
Preferred name:
NC_000007.13:g.(?_56079455)_(56085092_?)dup
HGVS:
NC_000007.13:g.(?_56079455)_(56085092_?)dup

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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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV002217585Invitae
criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))		Uncertain significance
(Sep 27, 2022) 		germlineclinical testing

PubMed (1)
[See all records that cite this PMID]

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Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineunknownnot providednot providednot providednot providednot providedclinical 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, SCV002217585.3

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (1)

Description

This variant results in a copy number gain of the genomic region encompassing exon(s) 6-8 of the PSPH gene. This region includes the termination codon of the gene. This copy number gain extends beyond the assayed region for this gene and therefore may encompass additional genes. As the precise location of this event is unknown, it may be in tandem or it may be located elsewhere in the genome. This variant has not been reported in the literature in individuals affected with PSPH-related conditions. Experimental studies and prediction algorithms are not available or were not evaluated, and the functional significance of this variant is currently unknown. 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.

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknownnot providednot providednot providednot providednot providednot providednot provided

Last Updated: Nov 11, 2023