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NC_000019.9:g.(?_33167170)_(36643309_?)dup AND Hereditary spastic paraplegia 75

Germline classification:
Uncertain significance (1 submission)
Last evaluated:
Aug 11, 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:
RCV003107659.3

Allele description [Variation Report for NC_000019.9:g.(?_33167170)_(36643309_?)dup]

NC_000019.9:g.(?_33167170)_(36643309_?)dup

Genes:
  • ATP4A:ATPase H+/K+ transporting subunit alpha [Gene - OMIM - HGNC]
  • CLIP3:CAP-Gly domain containing linker protein 3 [Gene - OMIM - HGNC]
  • CEBPA:CCAAT enhancer binding protein alpha [Gene - OMIM - HGNC]
  • CEBPG:CCAAT enhancer binding protein gamma [Gene - OMIM - HGNC]
  • CD22:CD22 molecule [Gene - OMIM - HGNC]
  • ETV2:ETS variant transcription factor 2 [Gene - OMIM - HGNC]
  • FAAP24:FA core complex associated protein 24 [Gene - OMIM - HGNC]
  • FXYD1:FXYD domain containing ion transport regulator 1 [Gene - OMIM - HGNC]
  • FXYD3:FXYD domain containing ion transport regulator 3 [Gene - OMIM - HGNC]
  • FXYD5:FXYD domain containing ion transport regulator 5 [Gene - OMIM - HGNC]
  • FXYD7:FXYD domain containing ion transport regulator 7 [Gene - OMIM - HGNC]
  • GPR42:G protein-coupled receptor 42 [Gene - OMIM - HGNC]
  • GPATCH1:G-patch domain containing 1 [Gene - HGNC]
  • GRAMD1A:GRAM domain containing 1A [Gene - OMIM - HGNC]
  • HAUS5:HAUS augmin like complex subunit 5 [Gene - OMIM - HGNC]
  • IGFLR1:IGF like family receptor 1 [Gene - OMIM - HGNC]
  • LRP3:LDL receptor related protein 3 [Gene - OMIM - HGNC]
  • LSM14A:LSM14A mRNA processing body assembly factor [Gene - OMIM - HGNC]
  • NFKBID:NFKB inhibitor delta [Gene - OMIM - HGNC]
  • NPHS1:NPHS1 adhesion molecule, nephrin [Gene - OMIM - HGNC]
  • RBM42:RNA binding motif protein 42 [Gene - OMIM - HGNC]
  • POLR2I:RNA polymerase II subunit I [Gene - OMIM - HGNC]
  • ARHGAP33:Rho GTPase activating protein 33 [Gene - OMIM - HGNC]
  • THAP8:THAP domain containing 8 [Gene - OMIM - HGNC]
  • U2AF1L4:U2 small nuclear RNA auxiliary factor 1 like 4 [Gene - OMIM - HGNC]
  • WDR62:WD repeat domain 62 [Gene - OMIM - HGNC]
  • WDR88:WD repeat domain 88 [Gene - HGNC]
  • WTIP:WT1 interacting protein [Gene - OMIM - HGNC]
  • ALKBH6:alkB homolog 6 [Gene - OMIM - HGNC]
  • APLP1:amyloid beta precursor like protein 1 [Gene - OMIM - HGNC]
  • CAPNS1:calpain small subunit 1 [Gene - OMIM - HGNC]
  • CHST8:carbohydrate sulfotransferase 8 [Gene - OMIM - HGNC]
  • CEP89:centrosomal protein 89 [Gene - OMIM - HGNC]
  • COX6B1:cytochrome c oxidase subunit 6B1 [Gene - OMIM - HGNC]
  • COX7A1:cytochrome c oxidase subunit 7A1 [Gene - OMIM - HGNC]
  • DMKN:dermokine [Gene - OMIM - HGNC]
  • FAM187B:family with sequence similarity 187 member B [Gene - HGNC]
  • FFAR1:free fatty acid receptor 1 [Gene - OMIM - HGNC]
  • FFAR2:free fatty acid receptor 2 [Gene - OMIM - HGNC]
  • FFAR3:free fatty acid receptor 3 [Gene - OMIM - HGNC]
  • GPI:glucose-6-phosphate isomerase [Gene - OMIM - HGNC]
  • GAPDHS:glyceraldehyde-3-phosphate dehydrogenase, spermatogenic [Gene - OMIM - HGNC]
  • GARRE1:granule associated Rac and RHOG effector 1 [Gene - OMIM - HGNC]
  • HSPB6:heat shock protein family B (small) member 6 [Gene - OMIM - HGNC]
  • HCST:hematopoietic cell signal transducer [Gene - OMIM - HGNC]
  • HAMP:hepcidin antimicrobial peptide [Gene - OMIM - HGNC]
  • HPN:hepsin [Gene - OMIM - HGNC]
  • KRTDAP:keratinocyte differentiation associated protein [Gene - OMIM - HGNC]
  • KIRREL2:kirre like nephrin family adhesion molecule 2 [Gene - OMIM - HGNC]
  • LGI4:leucine rich repeat LGI family member 4 [Gene - OMIM - HGNC]
  • LRFN3:leucine rich repeat and fibronectin type III domain containing 3 [Gene - OMIM - HGNC]
  • LIN37:lin-37 DREAM MuvB core complex component [Gene - HGNC]
  • LSR:lipolysis stimulated lipoprotein receptor [Gene - OMIM - HGNC]
  • KMT2B:lysine methyltransferase 2B [Gene - OMIM - HGNC]
  • MAG:myelin associated glycoprotein [Gene - OMIM - HGNC]
  • NUDT19:nudix hydrolase 19 [Gene - HGNC]
  • OVOL3:ovo like zinc finger 3 [Gene - OMIM - HGNC]
  • PEPD:peptidase D [Gene - OMIM - HGNC]
  • KCTD15:potassium channel tetramerization domain containing 15 [Gene - OMIM - HGNC]
  • PSENEN:presenilin enhancer, gamma-secretase subunit [Gene - OMIM - HGNC]
  • PDCD2L:programmed cell death 2 like [Gene - OMIM - HGNC]
  • PROSER3:proline and serine rich 3 [Gene - HGNC]
  • PRODH2:proline dehydrogenase 2 [Gene - OMIM - HGNC]
  • RGS9BP:regulator of G protein signaling 9 binding protein [Gene - OMIM - HGNC]
  • RHPN2:rhophilin Rho GTPase binding protein 2 [Gene - OMIM - HGNC]
  • SCGB2B2:secretoglobin family 2B member 2 [Gene - OMIM - HGNC]
  • SCN1B:sodium voltage-gated channel beta subunit 1 [Gene - OMIM - HGNC]
  • SLC7A10:solute carrier family 7 member 10 [Gene - OMIM - HGNC]
  • SLC7A9:solute carrier family 7 member 9 [Gene - OMIM - HGNC]
  • SYNE4:spectrin repeat containing nuclear envelope family member 4 [Gene - OMIM - HGNC]
  • SDHAF1:succinate dehydrogenase complex assembly factor 1 [Gene - OMIM - HGNC]
  • SBSN:suprabasin [Gene - OMIM - HGNC]
  • TYROBP:transmembrane immune signaling adaptor TYROBP [Gene - OMIM - HGNC]
  • TMEM147:transmembrane protein 147 [Gene - OMIM - HGNC]
  • TBCB:tubulin folding cofactor B [Gene - OMIM - HGNC]
  • TDRD12:tudor domain containing 12 [Gene - HGNC]
  • UBA2:ubiquitin like modifier activating enzyme 2 [Gene - OMIM - HGNC]
  • USF2:upstream transcription factor 2, c-fos interacting [Gene - OMIM - HGNC]
  • UPK1A:uroplakin 1A [Gene - OMIM - HGNC]
  • ZBTB32:zinc finger and BTB domain containing 32 [Gene - OMIM - HGNC]
  • ZNF181:zinc finger protein 181 [Gene - OMIM - HGNC]
  • ZNF302:zinc finger protein 302 [Gene - HGNC]
  • ZNF30:zinc finger protein 30 [Gene - HGNC]
  • ZNF599:zinc finger protein 599 [Gene - HGNC]
  • ZNF792:zinc finger protein 792 [Gene - HGNC]
Variant type:
Duplication
Cytogenetic location:
19q13.11-13.12
Genomic location:
Chr19: 33167170 - 36643309 (on Assembly GRCh37)
Preferred name:
NC_000019.9:g.(?_33167170)_(36643309_?)dup
HGVS:
NC_000019.9:g.(?_33167170)_(36643309_?)dup

Condition(s)

Name:
Hereditary spastic paraplegia 75
Synonyms:
Spastic paraplegia 75, autosomal recessive
Identifiers:
MONDO: MONDO:0014729; MedGen: C4225250; Orphanet: 459056; OMIM: 616680

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV003794650Invitae
criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))		Uncertain significance
(Aug 11, 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, SCV003794650.2

#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 MAG 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 MAG-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