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NC_000007.13:g.(?_56079455)_(56174106_?)del AND Deficiency of phosphoserine phosphatase

Germline classification:
Uncertain significance (1 submission)
Last evaluated:
Jan 15, 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:
RCV001920532.5

Allele description

NC_000007.13:g.(?_56079455)_(56174106_?)del

Genes:
CCT6A:chaperonin containing TCP1 subunit 6A [Gene - OMIM - HGNC]
CHCHD2:coiled-coil-helix-coiled-coil-helix domain containing 2 [Gene - OMIM - HGNC]
PHKG1:phosphorylase kinase catalytic subunit gamma 1 [Gene - OMIM - HGNC]
PSPH:phosphoserine phosphatase [Gene - OMIM - HGNC]
SUMF2:sulfatase modifying factor 2 [Gene - OMIM - HGNC]
Variant type:
Deletion
Cytogenetic location:
7p11.2
Genomic location:
Chr7: 56079455 - 56174106 (on Assembly GRCh37)
Preferred name:
NC_000007.13:g.(?_56079455)_(56174106_?)del
HGVS:
NC_000007.13:g.(?_56079455)_(56174106_?)del

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
SCV002186300Invitae
criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))		Uncertain significance
(Jan 15, 2022) 		germlineclinical testing

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

Help

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, SCV002186300.4

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

Description

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. This variant has not been reported in the literature in individuals affected with PSPH-related conditions. A gross deletion of the genomic region encompassing the full coding sequence of the PSPH gene has been identified. The current clinical and genetic evidence is not sufficient to establish whether loss-of-function variants in PSPH cause disease. The boundaries of this event are unknown as they extend beyond the assayed region for this gene and therefore may encompass additional genes.

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

Last Updated: Jun 9, 2024