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NM_001102564.3(IFT43):c.1A>G (p.Met1Val) AND not provided

Germline classification:
Pathogenic (1 submission)
Last evaluated:
May 20, 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:
RCV001852564.5

Allele description [Variation Report for NM_001102564.3(IFT43):c.1A>G (p.Met1Val)]

NM_001102564.3(IFT43):c.1A>G (p.Met1Val)

Gene:
IFT43:intraflagellar transport 43 [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
14q24.3
Genomic location:
Preferred name:
NM_001102564.3(IFT43):c.1A>G (p.Met1Val)
HGVS:
  • NC_000014.9:g.75985787A>G
  • NG_011715.1:g.963T>C
  • NG_031957.1:g.5035A>G
  • NM_001102564.3:c.1A>GMANE SELECT
  • NM_001255995.3:c.1A>G
  • NM_052873.3:c.1A>G
  • NP_001096034.1:p.Met1Val
  • NP_001242924.1:p.Met1Val
  • NP_443105.2:p.Met1Val
  • LRG_399:g.963T>C
  • NC_000014.8:g.76452130A>G
  • NM_052873.2:c.1A>G
  • NR_045664.2:n.25A>G
  • NR_045665.2:n.25A>G
Protein change:
M1V; MET1VAL
Links:
OMIM: 614068.0001; dbSNP: rs387907107
NCBI 1000 Genomes Browser:
rs387907107
Molecular consequence:
  • NM_001102564.3:c.1A>G - initiator_codon_variant - [Sequence Ontology: SO:0001582]
  • NM_001255995.3:c.1A>G - initiator_codon_variant - [Sequence Ontology: SO:0001582]
  • NM_052873.3:c.1A>G - initiator_codon_variant - [Sequence Ontology: SO:0001582]
  • NM_001102564.3:c.1A>G - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001255995.3:c.1A>G - missense variant - [Sequence Ontology: SO:0001583]
  • NM_052873.3:c.1A>G - missense variant - [Sequence Ontology: SO:0001583]
  • NR_045664.2:n.25A>G - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NR_045665.2:n.25A>G - non-coding transcript variant - [Sequence Ontology: SO:0001619]

Condition(s)

Synonyms:
none provided
Identifiers:
MedGen: C3661900

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV002238789Invitae
criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))
Pathogenic
(May 20, 2022)
germlineclinical testing

PubMed (4)
[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

C14ORF179 encoding IFT43 is mutated in Sensenbrenner syndrome.

Arts HH, Bongers EM, Mans DA, van Beersum SE, Oud MM, Bolat E, Spruijt L, Cornelissen EA, Schuurs-Hoeijmakers JH, de Leeuw N, Cormier-Daire V, Brunner HG, Knoers NV, Roepman R.

J Med Genet. 2011 Jun;48(6):390-5. doi: 10.1136/jmg.2011.088864. Epub 2011 Mar 4.

PubMed [citation]
PMID:
21378380

Mutations in IFT-A satellite core component genes IFT43 and IFT121 produce short rib polydactyly syndrome with distinctive campomelia.

Duran I, Taylor SP, Zhang W, Martin J, Qureshi F, Jacques SM, Wallerstein R, Lachman RS, Nickerson DA, Bamshad M, Cohn DH, Krakow D.

Cilia. 2017;6:7. doi: 10.1186/s13630-017-0051-y.

PubMed [citation]
PMID:
28400947
PMCID:
PMC5387211
See all PubMed Citations (4)

Details of each submission

From Invitae, SCV002238789.4

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (4)

Description

This sequence change affects the initiator methionine of the IFT43 mRNA. The next in-frame methionine is located at codon 22. For these reasons, this variant has been classified as Pathogenic. Experimental studies have shown that disruption of the initiator codon affects IFT43 function (PMID: 21378380). Algorithms developed to predict the effect of variants on protein structure and function are not available or were not evaluated for this variant. ClinVar contains an entry for this variant (Variation ID: 31098). Disruption of the initiator codon has been observed in individuals with Sensenbrenner syndrome and short rib polydactyly syndrome (PMID: 21378380, 28400947, 29896747). It has also been observed to segregate with disease in related individuals. This variant is not present in population databases (gnomAD no frequency).

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

Last Updated: Feb 14, 2024