NM_001177701.3(IFT27):c.527G>A (p.Arg176Gln) AND not provided

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Aug 22, 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:: RCV001978230.3

Allele description [Variation Report for NM_001177701.3(IFT27):c.527G>A (p.Arg176Gln)]

NM_001177701.3(IFT27):c.527G>A (p.Arg176Gln)

Genes:

CACNG2-DT:CACNG2 divergent transcript [Gene - HGNC]
IFT27:intraflagellar transport 27 [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

22q12.3

Genomic location:

Preferred name:

NM_001177701.3(IFT27):c.527G>A (p.Arg176Gln)

HGVS:

NC_000022.11:g.36758345C>T
NG_034205.1:g.22789G>A
NM_001177701.3:c.527G>AMANE SELECT
NM_001363003.2:c.527G>A
NM_006860.4:c.524G>A
NM_006860.5:c.524G>A
NP_001171172.1:p.Arg176Gln
NP_001349932.1:p.Arg176Gln
NP_006851.1:p.Arg175Gln
NC_000022.10:g.37154389C>T

Protein change:

R175Q

Links:

dbSNP: rs568701732

NCBI 1000 Genomes Browser:

rs568701732

Molecular consequence:

NM_001177701.3:c.527G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001363003.2:c.527G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_006860.5:c.524G>A - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Synonyms:: none provided
Identifiers:: MedGen: C3661900

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Homo sapiens ring finger protein, transmembrane 1 (RNFT1), mRNA
Homo sapiens ring finger protein, transmembrane 1 (RNFT1), mRNA
gi|1519245599|ref|NM_016125.4|

Nucleotide
Mainland tiger snake genome project
Mainland tiger snake genome project
De novo whole genome sequencing of the mainland tiger snake, Notechis scutatus

BioProject
TBC1D3P1 TBC1 domain family member 3 pseudogene 1 [Homo sapiens]
TBC1D3P1 TBC1 domain family member 3 pseudogene 1 [Homo sapiens]
Gene ID:400609

Gene

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV002274497	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (Aug 22, 2022)	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

SCV002274497

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(Aug 22, 2022)

germline

clinical testing

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	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, SCV002274497.2

#	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 arginine, which is basic and polar, with glutamine, which is neutral and polar, at codon 175 of the IFT27 protein (p.Arg175Gln). This variant is present in population databases (rs568701732, gnomAD 0.02%). This variant has not been reported in the literature in individuals affected with IFT27-related conditions. ClinVar contains an entry for this variant (Variation ID: 1489149). Advanced modeling of protein sequence and biophysical properties (such as structural, functional, and spatial information, amino acid conservation, physicochemical variation, residue mobility, and thermodynamic stability) performed at Invitae indicates that this missense variant is not expected to disrupt IFT27 protein function. 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.

#	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: Oct 13, 2024

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