NM_014014.5(SNRNP200):c.3260C>T (p.Ser1087Leu) AND not provided

Germline classification:: Pathogenic (2 submissions)
Last evaluated:: Aug 17, 2023
Review status:: 2 stars out of maximum of 4 stars
criteria provided, multiple submitters, no conflicts

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:: RCV001091895.28

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]

Observations:

Condition(s)

Synonyms:: none provided; RECLASSIFIED - ADRA2C POLYMORPHISM; RECLASSIFIED - ADRB1 POLYMORPHISM
Identifiers:: MedGen: C3661900

Recent activity

Clear Turn Off Turn On

Your browsing activity is empty.

Activity recording is turned off.

Turn recording back on

Help

Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV001248165	CeGaT Center for Human Genetics Tuebingen	criteria provided, single submitter (CeGaT Center For Human Genetics Tuebingen Variant Classification Criteria Version 2)	Pathogenic (Dec 1, 2017)	germline	clinical testing	Citation Link,
SCV001399508	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Pathogenic (Aug 17, 2023)	germline	clinical testing	PubMed (4) [See all records that cite these PMIDs] 28559085, 19878916, 24302620, 28492532

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV001248165

CeGaT Center for Human Genetics Tuebingen

criteria provided, single submitter

(CeGaT Center For Human Genetics Tuebingen Variant Classification Criteria Version 2)

Pathogenic
(Dec 1, 2017)

germline

clinical testing

Citation Link,

SCV001399508

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Pathogenic
(Aug 17, 2023)

germline

clinical testing

PubMed (4)
[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	2	not provided	not provided	not provided	not provided	clinical testing
not provided	germline	unknown	not provided	not provided	not provided	not provided	not provided	clinical testing

Citations

PubMed

Clinically Focused Molecular Investigation of 1000 Consecutive Families with Inherited Retinal Disease.

Stone EM, Andorf JL, Whitmore SS, DeLuca AP, Giacalone JC, Streb LM, Braun TA, Mullins RF, Scheetz TE, Sheffield VC, Tucker BA.

Ophthalmology. 2017 Sep;124(9):1314-1331. doi: 10.1016/j.ophtha.2017.04.008. Epub 2017 May 27.

PubMed [citation]

PMID:: 28559085
PMCID:: PMC5565704

Autosomal-dominant retinitis pigmentosa caused by a mutation in SNRNP200, a gene required for unwinding of U4/U6 snRNAs.

Zhao C, Bellur DL, Lu S, Zhao F, Grassi MA, Bowne SJ, Sullivan LS, Daiger SP, Chen LJ, Pang CP, Zhao K, Staley JP, Larsson C.

Am J Hum Genet. 2009 Nov;85(5):617-27. doi: 10.1016/j.ajhg.2009.09.020. Epub 2009 Oct 29.

PubMed [citation]

PMID:: 19878916
PMCID:: PMC2775825

See all PubMed Citations (4)

Details of each submission

From CeGaT Center for Human Genetics Tuebingen, SCV001248165.26

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

#	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		2	not provided	not provided	not provided

From Labcorp Genetics (formerly Invitae), Labcorp, SCV001399508.5

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (4)

Description

This missense change has been observed in individuals with autosomal dominant retinitis pigmentosa (PMID: 19878916, 28559085). It has also been observed to segregate with disease in related individuals. This sequence change replaces serine, which is neutral and polar, with leucine, which is neutral and non-polar, at codon 1087 of the SNRNP200 protein (p.Ser1087Leu). This variant is present in population databases (rs267607077, gnomAD 0.0009%). ClinVar contains an entry for this variant (Variation ID: 7928). An algorithm developed to predict the effect of missense changes on protein structure and function (PolyPhen-2) suggests that this variant is likely to be disruptive. Experimental studies have shown that this missense change affects SNRNP200 function (PMID: 19878916, 24302620). For these reasons, this variant has been classified as Pathogenic.

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

Last Updated: Nov 30, 2024

ClinVar

Relating variation to medicine