NM_014714.4(IFT140):c.3874-1G>A AND Saldino-Mainzer syndrome

Clinical significance:Likely pathogenic (Last evaluated: Sep 11, 2020)

Review status:1 star out of maximum of 4 stars

criteria provided, single submitter

Based on:
1 submission [Details]
Record status:
current
Accession:
RCV001234793.2

Allele description [Variation Report for NM_014714.4(IFT140):c.3874-1G>A]

NM_014714.4(IFT140):c.3874-1G>A

Gene:
IFT140:intraflagellar transport 140 [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
16p13.3
Genomic location:
Preferred name:
NM_014714.4(IFT140):c.3874-1G>A
HGVS:
  • NC_000016.10:g.1520048C>T
  • NG_032783.1:g.97061G>A
  • NM_014714.4:c.3874-1G>AMANE SELECT
  • NC_000016.9:g.1570049C>T
  • NM_014714.3:c.3874-1G>A
Molecular consequence:
  • NM_014714.4:c.3874-1G>A - splice acceptor variant - [Sequence Ontology: SO:0001574]

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

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV001407453Invitaecriteria provided, single submitter
Likely pathogenic
(Sep 11, 2020)
germlineclinical testing

PubMed (6)
[See all records that cite these PMIDs]

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineunknownnot providednot providednot providednot providednot providedclinical testing

Citations

PubMed

Splicing in action: assessing disease causing sequence changes.

Baralle D, Baralle M.

J Med Genet. 2005 Oct;42(10):737-48. Review.

PubMed [citation]
PMID:
16199547
PMCID:
PMC1735933

Mainzer-Saldino syndrome is a ciliopathy caused by IFT140 mutations.

Perrault I, Saunier S, Hanein S, Filhol E, Bizet AA, Collins F, Salih MA, Gerber S, Delphin N, Bigot K, Orssaud C, Silva E, Baudouin V, Oud MM, Shannon N, Le Merrer M, Roche O, Pietrement C, Goumid J, Baumann C, Bole-Feysot C, Nitschke P, et al.

Am J Hum Genet. 2012 May 4;90(5):864-70. doi: 10.1016/j.ajhg.2012.03.006. Epub 2012 Apr 12.

PubMed [citation]
PMID:
22503633
PMCID:
PMC3376548
See all PubMed Citations (6)

Details of each submission

From Invitae, SCV001407453.2

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (6)

Description

This sequence change affects an acceptor splice site in intron 28 of the IFT140 gene. It is expected to disrupt RNA splicing and likely results in an absent or disrupted protein product. This variant is present in population databases (rs749563050, ExAC 0.01%). This variant has not been reported in the literature in individuals with IFT140-related conditions. Donor and acceptor splice site variants typically lead to a loss of protein function (PMID: 16199547), and loss-of-function variants in IFT140 are known to be pathogenic (PMID: 22503633, 23418020, 24009529, 26216056). In summary, the currently available evidence indicates that the variant is pathogenic, but additional data are needed to prove that conclusively. Therefore, this variant has been classified as Likely Pathogenic.

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknownnot providednot providednot providednot providednot providednot providednot provided

Last Updated: May 10, 2021

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