NM_006269.2(RP1):c.2015del (p.Lys672fs) AND not provided

Germline classification:: Pathogenic (1 submission)
Last evaluated:: Jul 21, 2023
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:: RCV003694555.1

Allele description [Variation Report for NM_006269.2(RP1):c.2015del (p.Lys672fs)]

NM_006269.2(RP1):c.2015del (p.Lys672fs)

Gene:

RP1:RP1 axonemal microtubule associated [Gene - OMIM - HGNC]

Variant type:

Deletion

Cytogenetic location:

8q12.1

Genomic location:

Preferred name:

NM_006269.2(RP1):c.2015del (p.Lys672fs)

HGVS:

NC_000008.11:g.54625897del
NG_009840.2:g.14831del
NG_009840.3:g.71714del
NM_001375654.1:c.787+3609del
NM_006269.2:c.2015delMANE SELECT
NP_006260.1:p.Lys672fs
NC_000008.10:g.55538453del
NC_000008.10:g.55538457del

Protein change:

K672fs

Molecular consequence:

NM_006269.2:c.2015del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001375654.1:c.787+3609del - intron variant - [Sequence Ontology: SO:0001627]

Condition(s)

Synonyms:: none provided
Identifiers:: MedGen: C3661900

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gi|2440670462|gb|OQ385044.1|

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV004437251	Invitae	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Pathogenic (Jul 21, 2023)	germline	clinical testing	PubMed (6) [See all records that cite these PMIDs] 11527933, 19933189, 29425069, 30027431, 33681214, 28492532

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV004437251

Invitae

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Pathogenic
(Jul 21, 2023)

germline

clinical testing

PubMed (6)
[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	unknown	not provided	not provided	not provided	not provided	not provided	clinical testing

Citations

PubMed

Clinical features and mutations in patients with dominant retinitis pigmentosa-1 (RP1).

Berson EL, Grimsby JL, Adams SM, McGee TL, Sweklo E, Pierce EA, Sandberg MA, Dryja TP.

Invest Ophthalmol Vis Sci. 2001 Sep;42(10):2217-24.

PubMed [citation]

PMID:: 11527933

Compound heterozygosity of two novel truncation mutations in RP1 causing autosomal recessive retinitis pigmentosa.

Chen LJ, Lai TY, Tam PO, Chiang SW, Zhang X, Lam S, Lai RY, Lam DS, Pang CP.

Invest Ophthalmol Vis Sci. 2010 Apr;51(4):2236-42. doi: 10.1167/iovs.09-4437. Epub 2009 Nov 20.

PubMed [citation]

PMID:: 19933189

See all PubMed Citations (6)

Details of each submission

From Invitae, SCV004437251.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (6)

Description

For these reasons, this variant has been classified as Pathogenic. This variant disrupts the C-terminus of the RP1 protein. Many variants that disrupt this region have been reported in individuals with either autosomal dominant or autosomal recessive retinitis pigmentosa (PMID: 11527933, 19933189, 29425069, 30027431, 33681214). Therefore, variants that disrupt this region are expected to be disease-causing. This variant has not been reported in the literature in individuals affected with RP1-related conditions. This variant is not present in population databases (gnomAD no frequency). This sequence change creates a premature translational stop signal (p.Lys672Argfs*10) in the RP1 gene. While this is not anticipated to result in nonsense mediated decay, it is expected to disrupt the last 1485 amino acid(s) of the RP1 protein.

#	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: Feb 28, 2024

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