NM_015662.3(IFT172):c.790C>T (p.Arg264Trp) AND multiple conditions

This record was updated by the submitter. Please see the current version.

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Nov 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:: RCV001326322.4

Allele description

NM_015662.3(IFT172):c.790C>T (p.Arg264Trp)

Gene:

IFT172:intraflagellar transport 172 [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

2p23.3

Genomic location:

Preferred name:

NM_015662.3(IFT172):c.790C>T (p.Arg264Trp)

HGVS:

NC_000002.12:g.27480145G>A
NG_034068.1:g.14667C>T
NM_015662.3:c.790C>TMANE SELECT
NP_056477.1:p.Arg264Trp
NC_000002.11:g.27703012G>A
NM_015662.2:c.790C>T

Protein change:

R264W

Links:

dbSNP: rs750783565

NCBI 1000 Genomes Browser:

rs750783565

Molecular consequence:

NM_015662.3:c.790C>T - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Name:: Short-rib thoracic dysplasia 10 with or without polydactyly (SRTD10)
Identifiers:: MONDO: MONDO:0014284; MedGen: C3810175; Orphanet: 474; OMIM: 615630

Name:: Retinitis pigmentosa 71 (RP71)
Identifiers:: MONDO: MONDO:0014618; MedGen: C4225342; Orphanet: 791; OMIM: 616394

Recent activity

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MAG: Candidatus Giovannonibacteria bacterium RIFCSPLOWO2_02_FULL_43_37 rifcsplow...
MAG: Candidatus Giovannonibacteria bacterium RIFCSPLOWO2_02_FULL_43_37 rifcsplowo2_02_scaffold_680, whole genome shotgun sequence
gi|1083483329|gb|MFIJ01000020.1||gn :MFIJ01|rifcsplowo2_02_scaffold_680

Nucleotide
MAG: Candidatus Giovannonibacteria bacterium RIFCSPLOWO2_02_FULL_43_37 rifcsplow...
MAG: Candidatus Giovannonibacteria bacterium RIFCSPLOWO2_02_FULL_43_37 rifcsplowo2_02_scaffold_1697, whole genome shotgun sequence
gi|1083483912|gb|MFIJ01000001.1||gn :MFIJ01|rifcsplowo2_02_scaffold_1697

Nucleotide
Homo sapiens helicase, POLQ like (HELQ), transcript variant 1, mRNA
Homo sapiens helicase, POLQ like (HELQ), transcript variant 1, mRNA
gi|1844083921|ref|NM_133636.5|

Nucleotide
Chain M, Cytochrome c oxidase polypeptide 8H
Chain M, Cytochrome c oxidase polypeptide 8H
gi|224036269|pdb|2ZXW|M

Protein

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV001517348	Invitae	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (Nov 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

SCV001517348

Invitae

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(Nov 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 Invitae, SCV001517348.4

#	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. 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 IFT172 protein function. ClinVar contains an entry for this variant (Variation ID: 1025937). This variant has not been reported in the literature in individuals affected with IFT172-related conditions. This variant is present in population databases (rs750783565, gnomAD 0.003%). This sequence change replaces arginine, which is basic and polar, with tryptophan, which is neutral and slightly polar, at codon 264 of the IFT172 protein (p.Arg264Trp).

#	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: Mar 5, 2024

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