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Single allele AND multiple conditions

Germline classification:
Pathogenic (1 submission)
Last evaluated:
Apr 25, 2017
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:
RCV000677958.2

Allele description [Variation Report for Single allele]

Genes:
  • LOC129932134:ATAC-STARR-seq lymphoblastoid active region 2257 [Gene]
  • LOC129932135:ATAC-STARR-seq lymphoblastoid active region 2258 [Gene]
  • LOC129932137:ATAC-STARR-seq lymphoblastoid active region 2259 [Gene]
  • LOC129932138:ATAC-STARR-seq lymphoblastoid active region 2260 [Gene]
  • LOC129932139:ATAC-STARR-seq lymphoblastoid active region 2261 [Gene]
  • LOC129932140:ATAC-STARR-seq lymphoblastoid active region 2262 [Gene]
  • LOC129932141:ATAC-STARR-seq lymphoblastoid active region 2263 [Gene]
  • LOC129932144:ATAC-STARR-seq lymphoblastoid active region 2264 [Gene]
  • LOC129932146:ATAC-STARR-seq lymphoblastoid active region 2265 [Gene]
  • LOC129932147:ATAC-STARR-seq lymphoblastoid active region 2269 [Gene]
  • LOC129932148:ATAC-STARR-seq lymphoblastoid active region 2270 [Gene]
  • LOC129932149:ATAC-STARR-seq lymphoblastoid active region 2271 [Gene]
  • LOC129932150:ATAC-STARR-seq lymphoblastoid active region 2272 [Gene]
  • LOC129932151:ATAC-STARR-seq lymphoblastoid active region 2273 [Gene]
  • LOC129932136:ATAC-STARR-seq lymphoblastoid silent region 1651 [Gene]
  • LOC129932142:ATAC-STARR-seq lymphoblastoid silent region 1652 [Gene]
  • LOC129932143:ATAC-STARR-seq lymphoblastoid silent region 1653 [Gene]
  • LOC129932145:ATAC-STARR-seq lymphoblastoid silent region 1654 [Gene]
  • LOC126805961:BRD4-independent group 4 enhancer GRCh37_chr1:192795712-192796911 [Gene]
  • LOC111556116:HNF1 motif-containing MPRA enhancer 26 [Gene]
  • LOC120893169:MED14-independent group 3 enhancer GRCh37_chr1:193324401-193325600 [Gene]
  • LOC129388703:MPRA-validated peak601 silencer [Gene]
  • LOC129388704:MPRA-validated peak603 silencer [Gene]
  • LOC129388705:MPRA-validated peak604 silencer [Gene]
  • LOC129388706:MPRA-validated peak605 silencer [Gene]
  • LOC129388707:MPRA-validated peak609 silencer [Gene]
  • LOC129388708:MPRA-validated peak610 silencer [Gene]
  • LOC129388709:MPRA-validated peak612 silencer [Gene]
  • LOC129388710:MPRA-validated peak613 silencer [Gene]
  • LOC129388711:MPRA-validated peak614 silencer [Gene]
  • LOC129388712:MPRA-validated peak616 silencer [Gene]
  • LOC129388713:MPRA-validated peak617 silencer [Gene]
  • LOC132088601:Neanderthal introgressed variant-containing enhancer experimental_1434 [Gene]
  • LOC132090670:Neanderthal introgressed variant-containing enhancer experimental_1475 [Gene]
  • LOC132088602:Neanderthal introgressed variant-containing enhancer experimental_1503 [Gene]
  • LOC126805962:P300/CBP strongly-dependent group 1 enhancer GRCh37_chr1:193583455-193584654 [Gene]
  • RGS2-AS1:RSG2 antisense RNA 1 [Gene - HGNC]
  • RO60:Ro60, Y RNA binding protein [Gene - OMIM - HGNC]
  • LOC122149334:Sharpr-MPRA regulatory region 4625 [Gene]
  • LOC122149332:Sharpr-MPRA regulatory region 5305 [Gene]
  • LOC122149333:Sharpr-MPRA regulatory region 7925 [Gene]
  • B3GALT2:beta-1,3-galactosyltransferase 2 [Gene - OMIM - HGNC]
  • CDC73:cell division cycle 73 [Gene - OMIM - HGNC]
  • GLRX2:glutaredoxin 2 [Gene - OMIM - HGNC]
  • LINC01031:long intergenic non-protein coding RNA 1031 [Gene - HGNC]
  • LINC02770:long intergenic non-protein coding RNA 2770 [Gene - HGNC]
  • MIR1278:microRNA 1278 [Gene - HGNC]
  • MIR4426:microRNA 4426 [Gene - HGNC]
  • RGS13:regulator of G protein signaling 13 [Gene - OMIM - HGNC]
  • RGS18:regulator of G protein signaling 18 [Gene - OMIM - HGNC]
  • RGS1:regulator of G protein signaling 1 [Gene - OMIM - HGNC]
  • RGS21:regulator of G protein signaling 21 [Gene - OMIM - HGNC]
  • RGS2:regulator of G protein signaling 2 [Gene - OMIM - HGNC]
  • SCARNA18B:small Cajal body-specific RNA 18B [Gene - HGNC]
  • UCHL5:ubiquitin C-terminal hydrolase L5 [Gene - OMIM - HGNC]
Variant type:
Deletion
Cytogenetic location:
1q31.2-31.3
Genomic location:
HGVS:
  • NC_000001.11:g.191919194_194615758del
  • NC_000001.10:g.191888324_194584888del

Condition(s)

Name:
Hyperparathyroidism 1 (HRPT1)
Synonyms:
HYPERPARATHYROIDISM, FAMILIAL ISOLATED PRIMARY
Identifiers:
MONDO: MONDO:0007767; MedGen: C1840402; Orphanet: 99879; OMIM: 145000
Name:
Parathyroid carcinoma (PRTC)
Synonyms:
Parathyroid cancer; Parathyroid gland carcinoma; CDC73-Related Parathyroid Carcinoma
Identifiers:
MONDO: MONDO:0012004; MedGen: C0687150; Orphanet: 143; OMIM: 608266; Human Phenotype Ontology: HP:0006780
Name:
Hyperparathyroidism 2 with jaw tumors
Synonyms:
HYPERPARATHYROIDISM, FAMILIAL PRIMARY, WITH MULTIPLE OSSIFYING JAW FIBROMAS; HYPERPARATHYROIDISM-JAW TUMOR SYNDROME, HEREDITARY; Hyperparathyroidism 2
Identifiers:
MONDO: MONDO:0007768; MedGen: C1704981; Orphanet: 99880; OMIM: 145001

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV000804113Geisinger Autism and Developmental Medicine Institute, Geisinger Health System
criteria provided, single submitter

(ACMG CNV Guidelines, 2011)		Pathogenic
(Apr 25, 2017) 		unknownprovider interpretation

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

Help

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedunknownunknownnot providednot providednot providednot providednot providedprovider interpretation

Citations

PubMed

Large intragenic deletion of CDC73 (exons 4-10) in a three-generation hyperparathyroidism-jaw tumor (HPT-JT) syndrome family.

Guarnieri V, Seaberg RM, Kelly C, Jean Davidson M, Raphael S, Shuen AY, Baorda F, Palumbo O, Scillitani A, Hendy GN, Cole DEC.

BMC Med Genet. 2017 Aug 3;18(1):83. doi: 10.1186/s12881-017-0445-0. Erratum in: BMC Med Genet. 2017 Sep 13;18(1):99.

PubMed [citation]
PMID:
28774260
PMCID:
PMC5543551

American College of Medical Genetics standards and guidelines for interpretation and reporting of postnatal constitutional copy number variants.

Kearney HM, Thorland EC, Brown KK, Quintero-Rivera F, South ST; Working Group of the American College of Medical Genetics Laboratory Quality Assurance Committee..

Genet Med. 2011 Jul;13(7):680-5. doi: 10.1097/GIM.0b013e3182217a3a.

PubMed [citation]
PMID:
21681106

Details of each submission

From Geisinger Autism and Developmental Medicine Institute, Geisinger Health System, SCV000804113.2

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedprovider interpretation PubMed (2)

Description

This deletion was identified in a 13 year old female with borderline intellectual disability, motor coordination disorder, ADHD, skull anomalies, history of neonatal seizure, and amblyopia. The patient's biological parents are unavailable for parental studies. There is no known family history of parathyroid cancer or thyroid disease. Of note, the patient also carries a pathogenic deletion at 16p11.2.

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

Last Updated: Oct 14, 2023