NM_001177701.3(IFT27):c.352+1G>T AND IFT27-related disorder

Germline classification:: Likely pathogenic (1 submission)
Last evaluated:: Oct 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:: RCV003392548.5

Allele description [Variation Report for NM_001177701.3(IFT27):c.352+1G>T]

NM_001177701.3(IFT27):c.352+1G>T

Genes:

CACNG2-DT:CACNG2 divergent transcript [Gene - HGNC]
IFT27:intraflagellar transport 27 [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

22q12.3

Genomic location:

Preferred name:

NM_001177701.3(IFT27):c.352+1G>T

HGVS:

NC_000022.11:g.36763918C>A
NG_034205.1:g.17216G>T
NM_001177701.3:c.352+1G>TMANE SELECT
NM_001363003.2:c.352+1G>T
NM_006860.5:c.349+1G>T
NC_000022.10:g.37159962C>A
NM_006860.4:c.349+1G>T

Nucleotide change:

IVS5, G-T, +1

Links:

OMIM: 615870.0003; dbSNP: rs780659194

NCBI 1000 Genomes Browser:

rs780659194

Molecular consequence:

NM_001177701.3:c.352+1G>T - splice donor variant - [Sequence Ontology: SO:0001575]
NM_001363003.2:c.352+1G>T - splice donor variant - [Sequence Ontology: SO:0001575]
NM_006860.5:c.349+1G>T - splice donor variant - [Sequence Ontology: SO:0001575]

Condition(s)

Name:: IFT27-related disorder
Synonyms:: IFT27-related condition
Identifiers:

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV004120120	PreventionGenetics, part of Exact Sciences	criteria provided, single submitter (ACMG Guidelines, 2015)	Likely pathogenic (Oct 20, 2022)	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

SCV004120120

PreventionGenetics, part of Exact Sciences

criteria provided, single submitter

(ACMG Guidelines, 2015)

Likely pathogenic
(Oct 20, 2022)

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

Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology.

Richards S, Aziz N, Bale S, Bick D, Das S, Gastier-Foster J, Grody WW, Hegde M, Lyon E, Spector E, Voelkerding K, Rehm HL; ACMG Laboratory Quality Assurance Committee..

Genet Med. 2015 May;17(5):405-24. doi: 10.1038/gim.2015.30. Epub 2015 Mar 5.

PubMed [citation]

PMID:: 25741868
PMCID:: PMC4544753

Details of each submission

From PreventionGenetics, part of Exact Sciences, SCV004120120.1

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

Description

The IFT27 c.349+1G>T variant is predicted to disrupt the GT donor site and interfere with normal splicing. On an alternate transcript (NM_001177701.2), this variant is referred to as c.352+1G>T. This variant was reported in the compound heterozygous state in two individuals with features consistent with Bardet-Biedl syndrome (Schaefer et al. 2019. PubMed ID: 30761183; Quélin et al. 2018. PubMed ID: 29704304). This variant is reported in 0.019% of alleles in individuals of European (Non-Finnish) descent in gnomAD (http://gnomad.broadinstitute.org/variant/22-37159962-C-A). Variants that disrupt the consensus splice donor site in IFT27 are expected to be pathogenic. This variant is interpreted as likely 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: Sep 29, 2024

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