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NM_005869.4(CWC27):c.427C>T (p.Arg143Ter) AND Metaphyseal chondrodysplasia-retinitis pigmentosa syndrome

Germline classification:
Pathogenic (1 submission)
Last evaluated:
May 22, 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:
RCV002251087.1

Allele description [Variation Report for NM_005869.4(CWC27):c.427C>T (p.Arg143Ter)]

NM_005869.4(CWC27):c.427C>T (p.Arg143Ter)

Gene:
CWC27:CWC27 spliceosome associated cyclophilin [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
5q12.3
Genomic location:
Preferred name:
NM_005869.4(CWC27):c.427C>T (p.Arg143Ter)
HGVS:
  • NC_000005.10:g.64785511C>T
  • NM_001297644.1:c.427C>T
  • NM_001297645.2:c.427C>T
  • NM_001318000.2:c.427C>T
  • NM_001364478.1:c.427C>T
  • NM_005869.4:c.427C>TMANE SELECT
  • NP_001284573.1:p.Arg143Ter
  • NP_001284574.1:p.Arg143Ter
  • NP_001304929.1:p.Arg143Ter
  • NP_001351407.1:p.Arg143Ter
  • NP_005860.2:p.Arg143Ter
  • NC_000005.9:g.64081338C>T
Protein change:
R143*
Links:
dbSNP: rs773382223
NCBI 1000 Genomes Browser:
rs773382223
Molecular consequence:
  • NM_001297644.1:c.427C>T - nonsense - [Sequence Ontology: SO:0001587]
  • NM_001297645.2:c.427C>T - nonsense - [Sequence Ontology: SO:0001587]
  • NM_001318000.2:c.427C>T - nonsense - [Sequence Ontology: SO:0001587]
  • NM_001364478.1:c.427C>T - nonsense - [Sequence Ontology: SO:0001587]
  • NM_005869.4:c.427C>T - nonsense - [Sequence Ontology: SO:0001587]
Observations:
1

Condition(s)

Name:
Metaphyseal chondrodysplasia-retinitis pigmentosa syndrome
Synonyms:
Retinitis pigmentosa with or without skeletal anomalies
Identifiers:
MONDO: MONDO:0009598; MedGen: C1855188; Orphanet: 166035; OMIM: 250410

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV0025214833billion
criteria provided, single submitter

(ACMG Guidelines, 2015)		Pathogenic
(May 22, 2022) 		germlineclinical testing

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

Help

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineyes1not providednot provided1not providedclinical testing

Citations

PubMed

Mutations in the Spliceosome Component CWC27 Cause Retinal Degeneration with or without Additional Developmental Anomalies.

Xu M, Xie YA, Abouzeid H, Gordon CT, Fiorentino A, Sun Z, Lehman A, Osman IS, Dharmat R, Riveiro-Alvarez R, Bapst-Wicht L, Babino D, Arno G, Busetto V, Zhao L, Li H, Lopez-Martinez MA, Azevedo LF, Hubert L, Pontikos N, Eblimit A, Lorda-Sanchez I, et al.

Am J Hum Genet. 2017 Apr 6;100(4):592-604. doi: 10.1016/j.ajhg.2017.02.008. Epub 2017 Mar 9.

PubMed [citation]
PMID:
28285769
PMCID:
PMC5384039

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

Details of each submission

From 3billion, SCV002521483.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not provided1not providednot providedclinical testing PubMed (2)

Description

The variant is observed at an extremely low frequency in the gnomAD v2.1.1 dataset (total allele frequency: <0.001%). Stop-gained (nonsense): predicted to result in a loss or disruption of normal protein function through nonsense-mediated decay (NMD) or protein truncation. Multiple pathogenic variants are reported downstream of the variant. The variant has been reported to be associated with CWC27 related disorder (PMID: 28285769). And it has been reported to be in trans with a pathogenic variant as either compound heterozygous or homozygous in at least one similarly affected unrelated individual (PMID: 28285769). Therefore, this variant is classified as pathogenic according to the recommendation of ACMG/AMP guideline.

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineyes1not providednot provided1not providednot providednot provided

Last Updated: Sep 29, 2024