NM_020366.4(RPGRIP1):c.2020C>T (p.Pro674Ser) AND Retinitis pigmentosa

Germline classification:: Likely pathogenic (1 submission)
Last evaluated:: Apr 1, 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:: RCV001724826.3

Allele description [Variation Report for NM_020366.4(RPGRIP1):c.2020C>T (p.Pro674Ser)]

NM_020366.4(RPGRIP1):c.2020C>T (p.Pro674Ser)

Gene:

RPGRIP1:RPGR interacting protein 1 [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

14q11.2

Genomic location:

Preferred name:

NM_020366.4(RPGRIP1):c.2020C>T (p.Pro674Ser)

HGVS:

NC_000014.9:g.21324875C>T
NG_008933.1:g.41899C>T
NM_001377523.1:c.689-2748C>T
NM_001377948.1:c.946C>T
NM_001377949.1:c.796+150C>T
NM_001377950.1:c.689-2748C>T
NM_001377951.1:c.191-2748C>T
NM_020366.4:c.2020C>TMANE SELECT
NP_001364877.1:p.Pro316Ser
NP_065099.3:p.Pro674Ser
NC_000014.8:g.21793034C>T
NM_020366.3:c.2020C>T

Protein change:

P316S

Links:

dbSNP: rs1328030621

NCBI 1000 Genomes Browser:

rs1328030621

Molecular consequence:

NM_001377523.1:c.689-2748C>T - intron variant - [Sequence Ontology: SO:0001627]
NM_001377949.1:c.796+150C>T - intron variant - [Sequence Ontology: SO:0001627]
NM_001377950.1:c.689-2748C>T - intron variant - [Sequence Ontology: SO:0001627]
NM_001377951.1:c.191-2748C>T - intron variant - [Sequence Ontology: SO:0001627]
NM_001377948.1:c.946C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_020366.4:c.2020C>T - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Name:: Retinitis pigmentosa (RP)
Synonyms:: Tapetoretinal degeneration
Identifiers:: MONDO: MONDO:0019200; MeSH: D012174; MedGen: C0035334; Orphanet: 791; OMIM: 268000; OMIM: PS268000

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV001950378	Broad Center for Mendelian Genomics, Broad Institute of MIT and Harvard	criteria provided, single submitter (ACMG Guidelines, 2015)	Likely pathogenic (Apr 1, 2021)	germline	curation	PubMed (3) [See all records that cite these PMIDs] 28456785, 25741868, 34906470

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV001950378

Broad Center for Mendelian Genomics, Broad Institute of MIT and Harvard

criteria provided, single submitter

(ACMG Guidelines, 2015)

Likely pathogenic
(Apr 1, 2021)

germline

curation

PubMed (3)
[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	not provided	not provided	not provided	not provided	not provided	curation

Citations

PubMed

Targeted next generation sequencing identified novel mutations in RPGRIP1 associated with both retinitis pigmentosa and Leber's congenital amaurosis in unrelated Chinese patients.

Huang H, Wang Y, Chen H, Chen Y, Wu J, Chiang PW, Fan N, Su Y, Deng J, Chen D, Li Y, Zhang X, Zhang M, Liang S, Banerjee S, Qi M, Liu X.

Oncotarget. 2017 May 23;8(21):35176-35183. doi: 10.18632/oncotarget.17052.

PubMed [citation]

PMID:: 28456785
PMCID:: PMC5471044

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

See all PubMed Citations (3)

Details of each submission

From Broad Center for Mendelian Genomics, Broad Institute of MIT and Harvard, SCV001950378.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	curation	PubMed (3)

Description

The p.Pro674Ser variant in RPGRIP1 was identified in an individual with Retinitis pigmentosa, via a collaborative study between the Broad Institute's Center for Mendelian Genomics and the Pierce lab (https://oculargenomics.meei.harvard.edu/labs/pierce-lab/lab-members/). Through a review of available evidence we were able to apply the following criteria: PM2, PP3, PM1, PP1, PM3. Based on this evidence we have classified this variant as Likely Pathogenic. If you have any questions about the classification please reach out to the Pierce Lab.

#	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: Mar 30, 2024

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