NM_006269.2(RP1):c.4171del (p.Gln1391fs) AND not provided

Germline classification:: Pathogenic (1 submission)
Last evaluated:: Mar 11, 2022
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:: RCV002550239.2

Allele description [Variation Report for NM_006269.2(RP1):c.4171del (p.Gln1391fs)]

NM_006269.2(RP1):c.4171del (p.Gln1391fs)

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.4171del (p.Gln1391fs)

HGVS:

NC_000008.11:g.54628053del
NG_009840.2:g.16987del
NM_001375654.1:c.787+5765del
NM_006269.2:c.4171delMANE SELECT
NP_006260.1:p.Gln1391fs
NC_000008.10:g.55540613del
NM_006269.1:c.4171del

Protein change:

Q1391fs

Links:

dbSNP: rs2129317503

NCBI 1000 Genomes Browser:

rs2129317503

Molecular consequence:

NM_006269.2:c.4171del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001375654.1:c.787+5765del - intron variant - [Sequence Ontology: SO:0001627]

Condition(s)

Synonyms:: none provided
Identifiers:: MedGen: C3661900

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV002965312	Invitae	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Pathogenic (Mar 11, 2022)	germline	clinical testing	PubMed (7) [See all records that cite these PMIDs] 11527933, 19933189, 29425069, 30027431, 33681214, 32565670, 28492532

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV002965312

Invitae

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Pathogenic
(Mar 11, 2022)

germline

clinical testing

PubMed (7)
[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 (7)

Details of each submission

From Invitae, SCV002965312.2

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

Description

For these reasons, this variant has been classified as Pathogenic. This variant disrupts a region of the RP1 protein in which other variant(s) (p.Ile2061Serfs*12) have been determined to be pathogenic (PMID: 11527933, 19933189, 29425069, 30027431, 33681214). This suggests that this is a clinically significant region of the protein, and that variants that disrupt it are likely to be disease-causing. ClinVar contains an entry for this variant (Variation ID: 1065776). This variant is also known as c.4171delC (p.Gln1391Lysfs*7. This premature translational stop signal has been observed in individuals with autosomal recessive retinitis pigmentosa (PMID: 32565670; Invitae). This variant is not present in population databases (gnomAD no frequency). This sequence change creates a premature translational stop signal (p.Gln1391Lysfs*6) in the RP1 gene. While this is not anticipated to result in nonsense mediated decay, it is expected to disrupt the last 766 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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