NM_014714.4(IFT140):c.4341del (p.Arg1448fs) AND Saldino-Mainzer syndrome

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Jun 13, 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:: RCV001362672.5

Allele description [Variation Report for NM_014714.4(IFT140):c.4341del (p.Arg1448fs)]

NM_014714.4(IFT140):c.4341del (p.Arg1448fs)

Gene:

IFT140:intraflagellar transport 140 [Gene - OMIM - HGNC]

Variant type:

Deletion

Cytogenetic location:

16p13.3

Genomic location:

Preferred name:

NM_014714.4(IFT140):c.4341del (p.Arg1448fs)

HGVS:

NC_000016.10:g.1510993del
NG_032783.1:g.106117del
NG_050910.1:g.22650del
NM_014714.4:c.4341delMANE SELECT
NP_055529.2:p.Arg1448fs
NC_000016.9:g.1560993del
NC_000016.9:g.1560994del

Protein change:

R1448fs

Links:

dbSNP: rs1209319873

NCBI 1000 Genomes Browser:

rs1209319873

Molecular consequence:

NM_014714.4:c.4341del - frameshift variant - [Sequence Ontology: SO:0001589]

Condition(s)

Name:: Saldino-Mainzer syndrome (SRTD9)
Synonyms:: Renal dysplasia, retinal pigmentary dystrophy, cerebellar ataxia and skeletal dysplasia; Conorenal syndrome; SHORT-RIB THORACIC DYSPLASIA 9 WITH OR WITHOUT POLYDACTYLY; See all synonyms [MedGen]
Identifiers:: MONDO: MONDO:0009964; MedGen: C1849437; Orphanet: 140969; OMIM: 266920

Recent activity

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nuclear factor of activated T-cells, cytoplasmic 2 isoform a [Mus musculus]
nuclear factor of activated T-cells, cytoplasmic 2 isoform a [Mus musculus]
gi|81295418|ref|NP_035029.2|

Protein

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV001558702	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (Jun 13, 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

SCV001558702

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(Jun 13, 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, SCV001558702.4

#	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. Experimental studies and prediction algorithms are not available or were not evaluated, and the functional significance of this variant is currently unknown. This variant has not been reported in the literature in individuals with IFT140-related conditions. This variant is not present in population databases (ExAC no frequency). This sequence change results in a frameshift in the IFT140 gene (p.Arg1448Glyfs*90). While this is not anticipated to result in nonsense mediated decay, it is expected to disrupt the last 16 amino acids of the IFT140 protein and extend the protein by an additional 74 amino acids.

#	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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