NM_006269.2(RP1):c.2473_2474delinsTA (p.Ile825Tyr) AND not provided

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Jul 3, 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:: RCV002589764.4

Allele description [Variation Report for NM_006269.2(RP1):c.2473_2474delinsTA (p.Ile825Tyr)]

NM_006269.2(RP1):c.2473_2474delinsTA (p.Ile825Tyr)

Gene:

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

Variant type:

Indel

Cytogenetic location:

8q12.1

Genomic location:

Preferred name:

NM_006269.2(RP1):c.2473_2474delinsTA (p.Ile825Tyr)

HGVS:

NC_000008.11:g.54626355_54626356delinsTA
NG_009840.2:g.15289_15290delinsTA
NG_009840.3:g.72172_72173delinsTA
NM_001375654.1:c.787+4067_787+4068delinsTA
NM_006269.2:c.2473_2474delinsTAMANE SELECT
NP_006260.1:p.Ile825Tyr
NC_000008.10:g.55538915_55538916delinsTA

Protein change:

I825Y

Molecular consequence:

NM_001375654.1:c.787+4067_787+4068delinsTA - intron variant - [Sequence Ontology: SO:0001627]
NM_006269.2:c.2473_2474delinsTA - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Synonyms:: none provided
Identifiers:: MedGen: C3661900

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LOC127825128 [Homo sapiens]
LOC127825128 [Homo sapiens]
Gene ID:127825128

Gene
Iron-Dextran Complex
Iron-Dextran Complex
A complex of ferric oxyhydroxide with dextrans of 5000 to 7000 daltons in a viscous solution containing 50 mg/ml of iron. It is supplied as a parenteral preparation and is use...<br/>

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV002940820	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (Jul 3, 2023)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV002940820

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(Jul 3, 2023)

germline

clinical testing

PubMed (1)
[See all records that cite this PMID]

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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

Sherloc: a comprehensive refinement of the ACMG-AMP variant classification criteria.

Nykamp K, Anderson M, Powers M, Garcia J, Herrera B, Ho YY, Kobayashi Y, Patil N, Thusberg J, Westbrook M; Invitae Clinical Genomics Group., Topper S.

Genet Med. 2017 Oct;19(10):1105-1117. doi: 10.1038/gim.2017.37. Epub 2017 May 11. Erratum in: Genet Med. 2020 Jan;22(1):240. doi: 10.1038/s41436-019-0624-9.

PubMed [citation]

PMID:: 28492532
PMCID:: PMC5632818

Details of each submission

From Labcorp Genetics (formerly Invitae), Labcorp, SCV002940820.2

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

Description

This sequence change replaces isoleucine, which is neutral and non-polar, with tyrosine, which is neutral and polar, at codon 825 of the RP1 protein (p.Ile825Tyr). This variant is present in population databases (no rsID available, gnomAD 0.002%). In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. An algorithm developed to predict the effect of missense changes on protein structure and function (PolyPhen-2) suggests that this variant¬†is likely to be tolerated. ClinVar contains an entry for this variant (Variation ID: 1911297). This variant has not been reported in the literature in individuals affected with RP1-related conditions.

#	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: Sep 29, 2024

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