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

Germline classification:: Pathogenic (1 submission)
Last evaluated:: May 22, 2024
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:: RCV001852564.7

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; RECLASSIFIED - ADRA2C POLYMORPHISM; RECLASSIFIED - ADRB1 POLYMORPHISM
Identifiers:: MedGen: C3661900

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV002238789	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Pathogenic (May 22, 2024)	germline	clinical testing	PubMed (4) [See all records that cite these PMIDs] 28400947, 29896747, 21378380, 28492532

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV002238789

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Pathogenic
(May 22, 2024)

germline

clinical testing

PubMed (4)
[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

[Clinical features and mutational analysis of a case with Sensenbrenner syndrome].

Jia S, Yang J, He T, Li W, Luo X, Huang Y, Li C.

Zhonghua Yi Xue Yi Chuan Xue Za Zhi. 2018 Jun 10;35(3):426-428. doi: 10.3760/cma.j.issn.1003-9406.2018.03.027. Chinese.

PubMed [citation]

PMID:: 29896747

See all PubMed Citations (4)

Details of each submission

From Labcorp Genetics (formerly Invitae), Labcorp, SCV002238789.5

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical 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. This variant is not present in population databases (gnomAD no frequency). 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. ClinVar contains an entry for this variant (Variation ID: 31098). Algorithms developed to predict the effect of variants on gene product structure and function are not available or were not evaluated for this variant. Experimental studies have shown that disruption of the initiator codon affects IFT43 function (PMID: 21378380). For these reasons, this variant has been classified as Pathogenic.

#	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: Apr 7, 2025

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