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NC_000009.11:g.(?_34458984)_(35809462_?)dup AND Hyperphosphatasia with intellectual disability syndrome 2

Germline classification:
Uncertain significance (1 submission)
Last evaluated:
Nov 29, 2019
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:
RCV000540114.3

Allele description [Variation Report for NC_000009.11:g.(?_34458984)_(35809462_?)dup]

NC_000009.11:g.(?_34458984)_(35809462_?)dup

Genes:
  • ARID3C:AT-rich interaction domain 3C [Gene - OMIM - HGNC]
  • CCL19:C-C motif chemokine ligand 19 [Gene - OMIM - HGNC]
  • CCL21:C-C motif chemokine ligand 21 [Gene - OMIM - HGNC]
  • CCL27:C-C motif chemokine ligand 27 [Gene - OMIM - HGNC]
  • CD72:CD72 molecule [Gene - OMIM - HGNC]
  • DNAJB5:DnaJ heat shock protein family (Hsp40) member B5 [Gene - OMIM - HGNC]
  • FANCG:FA complementation group G [Gene - OMIM - HGNC]
  • PHF24:PHD finger protein 24 [Gene - OMIM - HGNC]
  • RGP1:RGP1 homolog, RAB6A GEF complex partner 1 [Gene - OMIM - HGNC]
  • RMRP:RNA component of mitochondrial RNA processing endoribonuclease [Gene - OMIM - HGNC]
  • RUSC2:RUN and SH3 domain containing 2 [Gene - OMIM - HGNC]
  • ARHGEF39:Rho guanine nucleotide exchange factor 39 [Gene - HGNC]
  • SPATA31F1:SPATA31 subfamily F member 1 [Gene - HGNC]
  • SPATA31G1:SPATA31 subfamily G member 1 [Gene - HGNC]
  • ATOSB:atos homolog B [Gene - OMIM - HGNC]
  • CREB3:cAMP responsive element binding protein 3 [Gene - OMIM - HGNC]
  • CA9:carbonic anhydrase 9 [Gene - OMIM - HGNC]
  • CIMIP2B:ciliary microtubule inner protein 2B [Gene - HGNC]
  • CNTFR:ciliary neurotrophic factor receptor [Gene - OMIM - HGNC]
  • CCDC107:coiled-coil domain containing 107 [Gene - HGNC]
  • DCTN3:dynactin subunit 3 [Gene - OMIM - HGNC]
  • DNAI1:dynein axonemal intermediate chain 1 [Gene - OMIM - HGNC]
  • ENHO:energy homeostasis associated [Gene - OMIM - HGNC]
  • GALT:galactose-1-phosphate uridylyltransferase [Gene - OMIM - HGNC]
  • GBA2:glucosylceramidase beta 2 [Gene - OMIM - HGNC]
  • IL11RA:interleukin 11 receptor subunit alpha [Gene - OMIM - HGNC]
  • MSMP:microseminoprotein, prostate associated [Gene - OMIM - HGNC]
  • NPR2:natriuretic peptide receptor 2 [Gene - OMIM - HGNC]
  • PIGO:phosphatidylinositol glycan anchor biosynthesis class O [Gene - OMIM - HGNC]
  • RPP25L:ribonuclease P/MRP subunit p25 like [Gene - HGNC]
  • SIGMAR1:sigma non-opioid intracellular receptor 1 [Gene - OMIM - HGNC]
  • SIT1:signaling threshold regulating transmembrane adaptor 1 [Gene - OMIM - HGNC]
  • SPAG8:sperm associated antigen 8 [Gene - OMIM - HGNC]
  • STOML2:stomatin like 2 [Gene - OMIM - HGNC]
  • TLN1:talin 1 [Gene - OMIM - HGNC]
  • TESK1:testis associated actin remodelling kinase 1 [Gene - OMIM - HGNC]
  • TPM2:tropomyosin 2 [Gene - OMIM - HGNC]
  • UNC13B:unc-13 homolog B [Gene - OMIM - HGNC]
  • VCP:valosin containing protein [Gene - OMIM - HGNC]
Variant type:
Duplication
Cytogenetic location:
9p13.3
Genomic location:
Chr9: 34458984 - 35809462 (on Assembly GRCh37)
Preferred name:
NC_000009.11:g.(?_34458984)_(35809462_?)dup
HGVS:
NC_000009.11:g.(?_34458984)_(35809462_?)dup

Condition(s)

Name:
Hyperphosphatasia with intellectual disability syndrome 2 (HPMRS2)
Synonyms:
GLYCOSYLPHOSPHATIDYLINOSITOL BIOSYNTHESIS DEFECT 6; HYPERPHOSPHATASIA WITH IMPAIRED INTELLECTUAL DEVELOPMENT SYNDROME 2
Identifiers:
MONDO: MONDO:0013882; MedGen: C3553637; Orphanet: 247262; OMIM: 614749

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV000652670Labcorp Genetics (formerly Invitae), Labcorp
criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))		Uncertain significance
(Nov 29, 2019) 		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 Labcorp Genetics (formerly Invitae), Labcorp, SCV000652670.2

#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 the full coding sequence of the PIGO gene. The boundaries of this event are unknown as they extend 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 with PIGO-related conditions. 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: Apr 7, 2025