NM_001102564.3(IFT43):c.2T>A (p.Met1Lys) AND not provided

Germline classification:: Pathogenic (1 submission)
Last evaluated:: Sep 18, 2019
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:: RCV001206016.7

Allele description [Variation Report for NM_001102564.3(IFT43):c.2T>A (p.Met1Lys)]

NM_001102564.3(IFT43):c.2T>A (p.Met1Lys)

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.2T>A (p.Met1Lys)

HGVS:

NC_000014.9:g.75985788T>A
NG_011715.1:g.962A>T
NG_031957.1:g.5036T>A
NM_001102564.3:c.2T>AMANE SELECT
NM_001255995.3:c.2T>A
NM_052873.3:c.2T>A
NP_001096034.1:p.Met1Lys
NP_001242924.1:p.Met1Lys
NP_443105.2:p.Met1Lys
LRG_399:g.962A>T
NC_000014.8:g.76452131T>A
NM_052873.2:c.2T>A
NR_045664.2:n.26T>A
NR_045665.2:n.26T>A

Protein change:

M1K; MET1LYS

Links:

OMIM: 614068.0002; dbSNP: rs769724508

NCBI 1000 Genomes Browser:

rs769724508

Molecular consequence:

NM_001102564.3:c.2T>A - initiator_codon_variant - [Sequence Ontology: SO:0001582]
NM_001255995.3:c.2T>A - initiator_codon_variant - [Sequence Ontology: SO:0001582]
NM_052873.3:c.2T>A - initiator_codon_variant - [Sequence Ontology: SO:0001582]
NM_001102564.3:c.2T>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001255995.3:c.2T>A - missense variant - [Sequence Ontology: SO:0001583]
NM_052873.3:c.2T>A - missense variant - [Sequence Ontology: SO:0001583]
NR_045664.2:n.26T>A - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_045665.2:n.26T>A - non-coding transcript variant - [Sequence Ontology: SO:0001619]

Condition(s)

Synonyms:: none provided
Identifiers:: MedGen: C3661900

Recent activity

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H.vulgare agpp mRNA for ADP-glucose pyrophosphorylase small subunit
H.vulgare agpp mRNA for ADP-glucose pyrophosphorylase small subunit
gi|18887|emb|X62241.1|

Nucleotide

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV001377303	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Pathogenic (Sep 18, 2019)	germline	clinical testing	PubMed (3) [See all records that cite these PMIDs] 28400947, 21378380, 28492532

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV001377303

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Pathogenic
(Sep 18, 2019)

germline

clinical testing

PubMed (3)
[See all records that cite these PMIDs]

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

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

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

See all PubMed Citations (3)

Details of each submission

From Labcorp Genetics (formerly Invitae), Labcorp, SCV001377303.5

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (3)

Description

For these reasons, this variant has been classified as Pathogenic. Disruption of the initiator codon has been observed to segregate with short rib polydactyly syndrome and cranioectodermal dysplasia in families (PMID: 28400947, 21378380). ClinVar contains an entry for this variant (Variation ID: 488649). This variant is not present in population databases (ExAC no frequency). This sequence change affects the initiator methionine of the IFT43 mRNA. The next in-frame methionine is located at codon 22.

#	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

ClinVar

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