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NM_014014.5(SNRNP200):c.3260C>T (p.Ser1087Leu) AND Retinitis pigmentosa 33

Germline classification:
Pathogenic (3 submissions)
Last evaluated:
Apr 8, 2021
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:
RCV000008390.8

Allele description [Variation Report for NM_014014.5(SNRNP200):c.3260C>T (p.Ser1087Leu)]

NM_014014.5(SNRNP200):c.3260C>T (p.Ser1087Leu)

Gene:
SNRNP200:small nuclear ribonucleoprotein U5 subunit 200 [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
2q11.2
Genomic location:
Preferred name:
NM_014014.5(SNRNP200):c.3260C>T (p.Ser1087Leu)
HGVS:
  • NC_000002.12:g.96287968G>A
  • NG_016973.1:g.22592C>T
  • NM_014014.5:c.3260C>TMANE SELECT
  • NP_054733.2:p.Ser1087Leu
  • NC_000002.11:g.96953706G>A
  • NM_014014.3:c.3260C>T
  • NM_014014.4:c.3260C>T
  • O75643:p.Ser1087Leu
Protein change:
S1087L; SER1087LEU
Links:
UniProtKB: O75643#VAR_063539; OMIM: 601664.0001; dbSNP: rs267607077
NCBI 1000 Genomes Browser:
rs267607077
Molecular consequence:
  • NM_014014.5:c.3260C>T - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Name:
Retinitis pigmentosa 33 (RP33)
Synonyms:
RP 33
Identifiers:
MONDO: MONDO:0012477; MedGen: C1835895; Orphanet: 791; OMIM: 610359

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV000028598OMIM
no assertion criteria provided
Pathogenic
(Mar 1, 2014)
germlineliterature only

PubMed (3)
[See all records that cite these PMIDs]

SCV001573276Ocular Genomics Institute, Massachusetts Eye and Ear
criteria provided, single submitter

(ACMG Guidelines, 2015)
Pathogenic
(Apr 8, 2021)
germlineresearch

PubMed (5)
[See all records that cite these PMIDs]

SCV001760098Genomics England Pilot Project, Genomics England
no assertion criteria provided

(ACGS Guidelines, 2016)
Pathogenicgermlineclinical testing

Citation Link

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineyesnot providednot providednot providednot providednot providedclinical testing, research
not providedgermlinenot providednot providednot providednot providednot providednot providedliterature only

Citations

PubMed

A novel locus (RP33) for autosomal dominant retinitis pigmentosa mapping to chromosomal region 2cen-q12.1.

Zhao C, Lu S, Zhou X, Zhang X, Zhao K, Larsson C.

Hum Genet. 2006 Jul;119(6):617-23. Epub 2006 Apr 13.

PubMed [citation]
PMID:
16612614

Comprehensive Rare Variant Analysis via Whole-Genome Sequencing to Determine the Molecular Pathology of Inherited Retinal Disease.

Carss KJ, Arno G, Erwood M, Stephens J, Sanchis-Juan A, Hull S, Megy K, Grozeva D, Dewhurst E, Malka S, Plagnol V, Penkett C, Stirrups K, Rizzo R, Wright G, Josifova D, Bitner-Glindzicz M, Scott RH, Clement E, Allen L, Armstrong R, Brady AF, et al.

Am J Hum Genet. 2017 Jan 5;100(1):75-90. doi: 10.1016/j.ajhg.2016.12.003. Epub 2016 Dec 29.

PubMed [citation]
PMID:
28041643
PMCID:
PMC5223092
See all PubMed Citations (6)

Details of each submission

From OMIM, SCV000028598.3

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedliterature only PubMed (3)

Description

In 12 affected members of a 4-generation Chinese family with autosomal dominant retinitis pigmentosa mapping to chromosome 2cen-q12.1 (RP33; 610359), previously studied by Zhao et al. (2006), Zhao et al. (2009) identified a 3260C-T transition in exon 25 of the SNRNP200 gene, resulting in a ser1087-to-leu (S1087L) substitution at a highly conserved residue within the 'ratchet' helix of the first Sec63 domain. The mutation was not found in 13 unaffected family members or in 400 unaffected controls. Assays in budding yeast revealed that a mutation corresponding to S1087L markedly impaired ATP-dependent unwinding of U4/U6 small nuclear RNAs.

Cvackova et al. (2014) found that the S1087L substitution had no effect on targeting of BBR2 to nuclear speckles or incorporation of BRR2 into snRNPs. However, the mutation reduced the time with which BRR2 interacted with pre-mRNAs during splicing and increased the use of cryptic splice sites in a reporter based on the beta-globin gene (HBB; 141900). Splicing of other reporter genes was not affected, suggesting gene-specific effects of the mutation on 5-prime splice site selection.

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

From Ocular Genomics Institute, Massachusetts Eye and Ear, SCV001573276.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedresearch PubMed (5)

Description

The SNRNP200 c.3260C>T variant was identified in an individual with retinitis pigmentosa with a presumed dominant inheritance pattern. Through a review of available evidence we were able to apply the following criteria: PS3, PM1, PM2, PP1, PP3. Based on this evidence we have classified this variant as Pathogenic.

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

From Genomics England Pilot Project, Genomics England, SCV001760098.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testingnot provided
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineyesnot providednot providednot providednot providednot providednot providednot provided

Last Updated: Nov 24, 2024