NM_183075.3(CYP2U1):c.311_336dup (p.Val113delinsArgCysSerTrpLeuThrTer) AND Hereditary spastic paraplegia 56

Germline classification:: Likely pathogenic (1 submission)
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:: RCV001251105.1

Allele description [Variation Report for NM_183075.3(CYP2U1):c.311_336dup (p.Val113delinsArgCysSerTrpLeuThrTer)]

NM_183075.3(CYP2U1):c.311_336dup (p.Val113delinsArgCysSerTrpLeuThrTer)

Genes:

CYP2U1-AS1:CYP2U1 and SGMS2 antisense RNA 1 [Gene - HGNC]
CYP2U1:cytochrome P450 family 2 subfamily U member 1 [Gene - OMIM - HGNC]

Variant type:

Duplication

Cytogenetic location:

4q25

Genomic location:

Preferred name:

NM_183075.3(CYP2U1):c.311_336dup (p.Val113delinsArgCysSerTrpLeuThrTer)

HGVS:

NC_000004.12:g.107931954_107931979dup
NG_007961.1:g.5394_5419dup
NM_183075.3:c.311_336dupMANE SELECT
NP_898898.1:p.Val113delinsArgCysSerTrpLeuThrTer
NC_000004.11:g.108853110_108853135dup
NM_183075.2:c.311_336dup

Links:

dbSNP: rs1733002976

NCBI 1000 Genomes Browser:

rs1733002976

Molecular consequence:

NM_183075.3:c.311_336dup - nonsense - [Sequence Ontology: SO:0001587]

Condition(s)

Name:: Hereditary spastic paraplegia 56
Synonyms:: Spastic paraplegia 56, autosomal recessive; SPASTIC PARAPLEGIA 56, AUTOSOMAL RECESSIVE, WITH OR WITHOUT PSEUDOXANTHOMA ELASTICUM; Spastic Paraplegia 56
Identifiers:: MONDO: MONDO:0014015; MedGen: C3539507; Orphanet: 320411; OMIM: 615030

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Tulasnella sp. AP-79c internal transcribed spacer 1, partial sequence; 5.8S ribo...
Tulasnella sp. AP-79c internal transcribed spacer 1, partial sequence; 5.8S ribosomal RNA gene, complete sequence; and internal transcribed spacer 2, partial sequence
gi|112430806|gb|DQ834399.1|

Nucleotide
Tulasnellaceae large subunit ribosomal RNA gene, partial sequence; mitochondrial...
Tulasnellaceae large subunit ribosomal RNA gene, partial sequence; mitochondrial.
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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV001426605	Centogene AG - the Rare Disease Company	criteria provided, single submitter (ACMG Guidelines, 2015)	Likely pathogenic	germline	clinical testing	PubMed (2) [See all records that cite these PMIDs] 25741868, 32860008

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV001426605

Centogene AG - the Rare Disease Company

criteria provided, single submitter

(ACMG Guidelines, 2015)

Likely pathogenic

germline

clinical testing

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

Help

Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	germline	yes	not provided	not provided	not provided	not provided	not provided	clinical testing

Citations

PubMed

Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology.

Richards S, Aziz N, Bale S, Bick D, Das S, Gastier-Foster J, Grody WW, Hegde M, Lyon E, Spector E, Voelkerding K, Rehm HL; ACMG Laboratory Quality Assurance Committee..

Genet Med. 2015 May;17(5):405-24. doi: 10.1038/gim.2015.30. Epub 2015 Mar 5.

PubMed [citation]

PMID:: 25741868
PMCID:: PMC4544753

Successful application of genome sequencing in a diagnostic setting: 1007 index cases from a clinically heterogeneous cohort.

Bertoli-Avella AM, Beetz C, Ameziane N, Rocha ME, Guatibonza P, Pereira C, Calvo M, Herrera-Ordonez N, Segura-Castel M, Diego-Alvarez D, Zawada M, Kandaswamy KK, Werber M, Paknia O, Zielske S, Ugrinovski D, Warnack G, Kampe K, Iurașcu MI, Cozma C, Vogel F, Alhashem A, et al.

Eur J Hum Genet. 2021 Jan;29(1):141-153. doi: 10.1038/s41431-020-00713-9. Epub 2020 Aug 28.

PubMed [citation]

PMID:: 32860008
PMCID:: PMC7852664

Details of each submission

From Centogene AG - the Rare Disease Company, SCV001426605.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (2)

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	yes	not provided	not provided	not provided		not provided	not provided	not provided	not provided

Last Updated: Dec 9, 2023

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