NM_001177701.3(IFT27):c.199G>A (p.Gly67Ser) AND not provided

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Aug 10, 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:: RCV002583314.3

Allele description [Variation Report for NM_001177701.3(IFT27):c.199G>A (p.Gly67Ser)]

NM_001177701.3(IFT27):c.199G>A (p.Gly67Ser)

Genes:

CACNG2-DT:CACNG2 divergent transcript [Gene - HGNC]
LOC126863139:CDK7 strongly-dependent group 2 enhancer GRCh37_chr22:37161913-37163112 [Gene]
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.199G>A (p.Gly67Ser)

HGVS:

NC_000022.11:g.36766173C>T
NG_034205.1:g.14961G>A
NG_087635.1:g.405C>T
NM_001177701.3:c.199G>AMANE SELECT
NM_001363003.2:c.199G>A
NM_006860.4:c.196G>A
NM_006860.5:c.196G>A
NP_001171172.1:p.Gly67Ser
NP_001349932.1:p.Gly67Ser
NP_006851.1:p.Gly66Ser
NC_000022.10:g.37162217C>T

Protein change:

G66S

Molecular consequence:

NM_001177701.3:c.199G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001363003.2:c.199G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_006860.5:c.196G>A - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Synonyms:: none provided
Identifiers:: MedGen: C3661900

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Caenorhabditis elegans Nuclear hormone receptor family member nhr-49 (nhr-49), m...
Caenorhabditis elegans Nuclear hormone receptor family member nhr-49 (nhr-49), mRNA
gi|1972232304|ref|NM_060212.8|

Nucleotide
Btn2p [Saccharomyces cerevisiae S288C]
Btn2p [Saccharomyces cerevisiae S288C]
gi|398365869|ref|NP_011658.3|

Protein

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV002939099	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (Aug 10, 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

SCV002939099

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(Aug 10, 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, SCV002939099.2

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

Description

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. Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant may disrupt the consensus splice site. 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 expected to disrupt IFT27 protein function. This variant has not been reported in the literature in individuals affected with IFT27-related conditions. This variant is present in population databases (rs772753691, gnomAD 0.03%). This sequence change replaces glycine, which is neutral and non-polar, with serine, which is neutral and polar, at codon 66 of the IFT27 protein (p.Gly66Ser).

#	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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