U.S. flag

An official website of the United States government

NC_000002.11:g.(?_231033840)_(234978657_?)dup AND Joubert syndrome 22

Germline classification:
Uncertain significance (1 submission)
Last evaluated:
Sep 19, 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:
RCV001877690.4

Allele description [Variation Report for NC_000002.11:g.(?_231033840)_(234978657_?)dup]

NC_000002.11:g.(?_231033840)_(234978657_?)dup

Genes:
  • HTR2B:5-hydroxytryptamine receptor 2B [Gene - OMIM - HGNC]
  • COPS7B:COP9 signalosome subunit 7B [Gene - OMIM - HGNC]
  • DIS3L2:DIS3 like 3'-5' exoribonuclease 2 [Gene - OMIM - HGNC]
  • DNAJB3:DnaJ heat shock protein family (Hsp40) member B3 [Gene - HGNC]
  • EFHD1:EF-hand domain family member D1 [Gene - OMIM - HGNC]
  • GPR55:G protein-coupled receptor 55 [Gene - OMIM - HGNC]
  • GIGYF2:GRB10 interacting GYF protein 2 [Gene - OMIM - HGNC]
  • HJURP:Holliday junction recognition protein [Gene - OMIM - HGNC]
  • SAG:S-antigen visual arrestin [Gene - OMIM - HGNC]
  • SP100:SP100 nuclear antigen [Gene - OMIM - HGNC]
  • SP110:SP110 nuclear body protein [Gene - OMIM - HGNC]
  • SP140L:SP140 nuclear body protein like [Gene - OMIM - HGNC]
  • SP140:SP140 nuclear body protein [Gene - OMIM - HGNC]
  • UGT1A10:UDP glucuronosyltransferase family 1 member A10 [Gene - OMIM - HGNC]
  • UGT1A1:UDP glucuronosyltransferase family 1 member A1 [Gene - OMIM - HGNC]
  • UGT1A3:UDP glucuronosyltransferase family 1 member A3 [Gene - OMIM - HGNC]
  • UGT1A4:UDP glucuronosyltransferase family 1 member A4 [Gene - OMIM - HGNC]
  • UGT1A5:UDP glucuronosyltransferase family 1 member A5 [Gene - OMIM - HGNC]
  • UGT1A6:UDP glucuronosyltransferase family 1 member A6 [Gene - OMIM - HGNC]
  • UGT1A7:UDP glucuronosyltransferase family 1 member A7 [Gene - OMIM - HGNC]
  • UGT1A8:UDP glucuronosyltransferase family 1 member A8 [Gene - OMIM - HGNC]
  • UGT1A9:UDP glucuronosyltransferase family 1 member A9 [Gene - OMIM - HGNC]
  • B3GNT7:UDP-GlcNAc:betaGal beta-1,3-N-acetylglucosaminyltransferase 7 [Gene - OMIM - HGNC]
  • ALPG:alkaline phosphatase, germ cell [Gene - OMIM - HGNC]
  • ALPI:alkaline phosphatase, intestinal [Gene - OMIM - HGNC]
  • ALPP:alkaline phosphatase, placental [Gene - OMIM - HGNC]
  • ARMC9:armadillo repeat containing 9 [Gene - OMIM - HGNC]
  • ATG16L1:autophagy related 16 like 1 [Gene - OMIM - HGNC]
  • CAB39:calcium binding protein 39 [Gene - OMIM - HGNC]
  • CHRND:cholinergic receptor nicotinic delta subunit [Gene - OMIM - HGNC]
  • CHRNG:cholinergic receptor nicotinic gamma subunit [Gene - OMIM - HGNC]
  • C2orf72:chromosome 2 open reading frame 72 [Gene - HGNC]
  • DGKD:diacylglycerol kinase delta [Gene - OMIM - HGNC]
  • ECEL1:endothelin converting enzyme like 1 [Gene - OMIM - HGNC]
  • EIF4E2:eukaryotic translation initiation factor 4E family member 2 [Gene - OMIM - HGNC]
  • ITM2C:integral membrane protein 2C [Gene - OMIM - HGNC]
  • MROH2A:maestro heat like repeat family member 2A [Gene - HGNC]
  • NPPC:natriuretic peptide C [Gene - OMIM - HGNC]
  • NEU2:neuraminidase 2 [Gene - OMIM - HGNC]
  • NMUR1:neuromedin U receptor 1 [Gene - OMIM - HGNC]
  • NGEF:neuronal guanine nucleotide exchange factor [Gene - OMIM - HGNC]
  • NCL:nucleolin [Gene - OMIM - HGNC]
  • PDE6D:phosphodiesterase 6D [Gene - OMIM - HGNC]
  • KCNJ13:potassium inwardly rectifying channel subfamily J member 13 [Gene - OMIM - HGNC]
  • PSMD1:proteasome 26S subunit, non-ATPase 1 [Gene - OMIM - HGNC]
  • PTMA:prothymosin alpha [Gene - OMIM - HGNC]
  • SNORC:secondary ossification center associated regulator of chondrocyte maturation [Gene - HGNC]
  • SPP2:secreted phosphoprotein 2 [Gene - OMIM - HGNC]
  • PRSS56:serine protease 56 [Gene - OMIM - HGNC]
  • SNORD20:small nucleolar RNA, C/D box 20 [Gene - OMIM - HGNC]
  • SNORD82:small nucleolar RNA, C/D box 82 [Gene - OMIM - HGNC]
  • SPATA3:spermatogenesis associated 3 [Gene - OMIM - HGNC]
  • TEX44:testis expressed 44 [Gene - HGNC]
  • TIGD1:tigger transposable element derived 1 [Gene - OMIM - HGNC]
  • TRPM8:transient receptor potential cation channel subfamily M member 8 [Gene - OMIM - HGNC]
  • USP40:ubiquitin specific peptidase 40 [Gene - OMIM - HGNC]
Variant type:
Duplication
Cytogenetic location:
2q37.1
Genomic location:
Chr2: 231033840 - 234978657 (on Assembly GRCh37)
Preferred name:
NC_000002.11:g.(?_231033840)_(234978657_?)dup
HGVS:
NC_000002.11:g.(?_231033840)_(234978657_?)dup

Condition(s)

Name:
Joubert syndrome 22 (JBTS22)
Identifiers:
MONDO: MONDO:0014297; MedGen: C3810278; Orphanet: 2754; OMIM: 615665

Recent activity

Clear Turn Off Turn On

Your browsing activity is empty.

Activity recording is turned off.

Turn recording back on

See more...

Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV002141010Invitae
criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))		Uncertain significance
(Sep 19, 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):240-242.

PubMed [citation]
PMID:
28492532
PMCID:
PMC5632818

Details of each submission

From Invitae, SCV002141010.3

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

Description

A copy number gain of the genomic region encompassing the full coding sequence of the PDE6D gene has been identified. 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 affected with PDE6D-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: Nov 11, 2023