NM_001177701.3(IFT27):c.428T>C (p.Leu143Pro) AND not provided

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Aug 19, 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:: RCV002001651.3

Allele description [Variation Report for NM_001177701.3(IFT27):c.428T>C (p.Leu143Pro)]

NM_001177701.3(IFT27):c.428T>C (p.Leu143Pro)

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.428T>C (p.Leu143Pro)

HGVS:

NC_000022.11:g.36762938A>G
NG_034205.1:g.18196T>C
NM_001177701.3:c.428T>CMANE SELECT
NM_001363003.2:c.428T>C
NM_006860.5:c.425T>C
NP_001171172.1:p.Leu143Pro
NP_001349932.1:p.Leu143Pro
NP_006851.1:p.Leu142Pro
NC_000022.10:g.37158982A>G

Protein change:

L142P

Links:

dbSNP: rs1429917517

NCBI 1000 Genomes Browser:

rs1429917517

Molecular consequence:

NM_001177701.3:c.428T>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001363003.2:c.428T>C - missense variant - [Sequence Ontology: SO:0001583]
NM_006860.5:c.425T>C - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Synonyms:: none provided
Identifiers:: MedGen: C3661900

Recent activity

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MIMAG Metagenome-assembled Genome sample from Syntrophobacteraceae bacterium
MIMAG Metagenome-assembled Genome sample from Syntrophobacteraceae bacterium

biosample
NR LBD domain-containing protein [Caenorhabditis elegans]
NR LBD domain-containing protein [Caenorhabditis elegans]
gi|71987054|ref|NP_001022103.1|

Protein
3-galactosyl-N-acetylglucosaminide 4-alpha-L-fucosyltransferase FUT3 [Homo sapie...
3-galactosyl-N-acetylglucosaminide 4-alpha-L-fucosyltransferase FUT3 [Homo sapiens]
gi|1761000886|ref|NP_001091109.3|

Protein
tectonic-3 isoform 1 precursor [Mus musculus]
tectonic-3 isoform 1 precursor [Mus musculus]
gi|31541975|ref|NP_080536.2|

Protein

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV002272347	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (Aug 19, 2021)	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

SCV002272347

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(Aug 19, 2021)

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, SCV002272347.2

#	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 leucine with proline at codon 142 of the IFT27 protein (p.Leu142Pro). The leucine residue is moderately conserved and there is a moderate physicochemical difference between leucine and proline. This variant is not present in population databases (ExAC no frequency). This variant has not been reported in the literature in individuals affected with IFT27-related conditions. 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: Sep 29, 2024

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