NM_001034853.2(RPGR):c.3396C>T (p.Asn1132=) AND not provided

Germline classification:: Benign (4 submissions)
Last evaluated:: Aug 27, 2021
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:: RCV000132610.9

Allele description [Variation Report for NM_001034853.2(RPGR):c.3396C>T (p.Asn1132=)]

NM_001034853.2(RPGR):c.3396C>T (p.Asn1132=)

Gene:

RPGR:retinitis pigmentosa GTPase regulator [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

Xp11.4

Genomic location:

Preferred name:

NM_001034853.2(RPGR):c.3396C>T (p.Asn1132=)

HGVS:

NC_000023.11:g.38285603G>A
NG_009553.1:g.46933C>T
NM_000328.3:c.1905+1491C>T
NM_001034853.2:c.3396C>TMANE SELECT
NM_001367245.1:c.1902+1491C>T
NM_001367246.1:c.1719+1491C>T
NM_001367247.1:c.1572+5356C>T
NM_001367248.1:c.1602+5356C>T
NM_001367249.1:c.1569+5356C>T
NM_001367250.1:c.1569+5356C>T
NM_001367251.1:c.1386+5356C>T
NP_001030025.1:p.Asn1132=
NC_000023.10:g.38144856G>A
NM_001034853.1:c.3396C>T

Links:

dbSNP: rs12687163

NCBI 1000 Genomes Browser:

rs12687163

Molecular consequence:

NM_000328.3:c.1905+1491C>T - intron variant - [Sequence Ontology: SO:0001627]
NM_001367245.1:c.1902+1491C>T - intron variant - [Sequence Ontology: SO:0001627]
NM_001367246.1:c.1719+1491C>T - intron variant - [Sequence Ontology: SO:0001627]
NM_001367247.1:c.1572+5356C>T - intron variant - [Sequence Ontology: SO:0001627]
NM_001367248.1:c.1602+5356C>T - intron variant - [Sequence Ontology: SO:0001627]
NM_001367249.1:c.1569+5356C>T - intron variant - [Sequence Ontology: SO:0001627]
NM_001367250.1:c.1569+5356C>T - intron variant - [Sequence Ontology: SO:0001627]
NM_001367251.1:c.1386+5356C>T - intron variant - [Sequence Ontology: SO:0001627]
NM_001034853.2:c.3396C>T - synonymous variant - [Sequence Ontology: SO:0001819]

Condition(s)

Synonyms:: none provided
Identifiers:: MedGen: C3661900

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cytochrome c oxidase subunit 1, partial (mitochondrion) [Spizella pusilla]
cytochrome c oxidase subunit 1, partial (mitochondrion) [Spizella pusilla]
gi|1824874832|gb|QIQ54401.1|

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000172561	Department of Ophthalmology and Visual Sciences Kyoto University	no assertion criteria provided	probable-non-pathogenic	not provided	not provided
SCV000971090	GeneDx	criteria provided, single submitter (GeneDx Variant Classification (06012015))	Benign (Apr 26, 2018)	germline	clinical testing	Citation Link,
SCV002759564	PreventionGenetics, part of Exact Sciences	criteria provided, single submitter (ACMG Guidelines, 2015)	Benign (Aug 27, 2021)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]
SCV005276083	Breakthrough Genomics, Breakthrough Genomics	criteria provided, single submitter (ACMG Guidelines, 2015)	Benign	germline	not provided	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, not provided
not provided	germline	unknown	not provided	not provided	not provided	not provided	not provided	clinical testing
not provided	not provided	not provided	not provided	not provided	not provided	1	not provided	literature only

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

Details of each submission

From Department of Ophthalmology and Visual Sciences Kyoto University, SCV000172561.1

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

Description

Converted during submission to Likely benign.

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

From GeneDx, SCV000971090.1

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

Description

This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease.

#	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 PreventionGenetics, part of Exact Sciences, SCV002759564.1

#	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	germline	unknown	not provided	not provided	not provided		not provided	not provided	not provided	not provided

From Breakthrough Genomics, Breakthrough Genomics, SCV005276083.1

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

#	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: Sep 29, 2024

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