NM_206933.4(USH2A):c.12574C>T (p.Arg4192Cys) AND Retinitis pigmentosa 39

Germline classification:: Pathogenic/Likely pathogenic (4 submissions)
Last evaluated:: Mar 22, 2024
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:: RCV000678644.19

Allele description [Variation Report for NM_206933.4(USH2A):c.12574C>T (p.Arg4192Cys)]

NM_206933.4(USH2A):c.12574C>T (p.Arg4192Cys)

Gene:

USH2A:usherin [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

1q41

Genomic location:

Preferred name:

NM_206933.4(USH2A):c.12574C>T (p.Arg4192Cys)

HGVS:

NC_000001.11:g.215675337G>A
NG_009497.2:g.753112C>T
NM_206933.4:c.12574C>TMANE SELECT
NP_996816.3:p.Arg4192Cys
NC_000001.10:g.215848679G>A
NG_009497.1:g.753060C>T
NM_206933.2:c.12574C>T
NM_206933.3(USH2A):c.12574C>T
p.Arg4192Cys

Protein change:

R4192C

Links:

dbSNP: rs750396156

NCBI 1000 Genomes Browser:

rs750396156

Molecular consequence:

NM_206933.4:c.12574C>T - missense variant - [Sequence Ontology: SO:0001583]

Observations:

Condition(s)

Name:: Retinitis pigmentosa 39 (RP39)
Identifiers:: MONDO: MONDO:0013436; MedGen: C3151138; Orphanet: 791; OMIM: 613809

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000804733	Joint Genome Diagnostic Labs from Nijmegen and Maastricht, Radboudumc and MUMC+	no assertion criteria provided	Likely pathogenic (Sep 1, 2016)	unknown	clinical testing
SCV001573664	Ocular Genomics Institute, Massachusetts Eye and Ear	criteria provided, single submitter (ACMG Guidelines, 2015)	Likely pathogenic (Apr 8, 2021)	germline	research	PubMed (7) [See all records that cite these PMIDs] 24625443, 23940504, 27460420, 29912909, 24516651, 27157150, 25741868
SCV001760009	Genomics England Pilot Project, Genomics England	criteria provided, single submitter (ACGS Guidelines, 2016)	Likely pathogenic	germline	clinical testing	Citation Link,
SCV004208253	Baylor Genetics	criteria provided, single submitter (ACMG Guidelines, 2015)	Pathogenic (Mar 22, 2024)	unknown	clinical testing	PubMed (1) [See all records that cite this PMID]

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, research
not provided	unknown	yes	1	not provided	not provided	not provided	not provided	clinical testing
not provided	unknown	unknown	not provided	not provided	not provided	not provided	not provided	clinical testing

Citations

PubMed

Identity-by-descent-guided mutation analysis and exome sequencing in consanguineous families reveals unusual clinical and molecular findings in retinal dystrophy.

Coppieters F, Van Schil K, Bauwens M, Verdin H, De Jaegher A, Syx D, Sante T, Lefever S, Abdelmoula NB, Depasse F, Casteels I, de Ravel T, Meire F, Leroy BP, De Baere E.

Genet Med. 2014 Sep;16(9):671-80. doi: 10.1038/gim.2014.24. Epub 2014 Mar 13.

PubMed [citation]

PMID:: 24625443

Exome sequencing of index patients with retinal dystrophies as a tool for molecular diagnosis.

Corton M, Nishiguchi KM, Avila-Fernández A, Nikopoulos K, Riveiro-Alvarez R, Tatu SD, Ayuso C, Rivolta C.

PLoS One. 2013 Jun 14;8(6):e65574. doi: 10.1371/journal.pone.0065574. Print 2013. Erratum in: PLoS One. 2016 Mar 31;11(3):e0153121. doi: 10.1371/journal.pone.0153121.

PubMed [citation]

PMID:: 23940504
PMCID:: PMC3683009

See all PubMed Citations (7)

Details of each submission

From Joint Genome Diagnostic Labs from Nijmegen and Maastricht, Radboudumc and MUMC+, SCV000804733.2

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	1	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	unknown	yes	not provided	not provided	not provided		1	not provided	not provided	not provided

From Ocular Genomics Institute, Massachusetts Eye and Ear, SCV001573664.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	research	PubMed (7)

Description

The USH2A c.12574C>T variant was identified in an individual with retinitis pigmentosa with a presumed recessive inheritance pattern. Through a review of available evidence we were able to apply the following criteria: PM2, PM3, PP1, PP4, BP2. Based on this evidence we have classified this variant as Likely Pathogenic.

#	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

From Genomics England Pilot Project, Genomics England, SCV001760009.1

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

From Baylor Genetics, SCV004208253.2

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

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

Last Updated: Oct 26, 2024

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