NM_014714.4(IFT140):c.1246C>T (p.Gln416Ter) AND Retinitis pigmentosa 80

Germline classification:: Pathogenic (1 submission)
Last evaluated:: Feb 23, 2023
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:: RCV003152928.1

Allele description [Variation Report for NM_014714.4(IFT140):c.1246C>T (p.Gln416Ter)]

NM_014714.4(IFT140):c.1246C>T (p.Gln416Ter)

Genes:

IFT140:intraflagellar transport 140 [Gene - OMIM - HGNC]
LOC105371046:uncharacterized LOC105371046 [Gene]

Variant type:

single nucleotide variant

Cytogenetic location:

16p13.3

Genomic location:

Preferred name:

NM_014714.4(IFT140):c.1246C>T (p.Gln416Ter)

HGVS:

NC_000016.10:g.1584330G>A
NG_032783.1:g.32779C>T
NM_014714.4:c.1246C>TMANE SELECT
NP_055529.2:p.Gln416Ter
NC_000016.9:g.1634331G>A
NM_014714.3:c.1246C>T

Protein change:

Q416*

Molecular consequence:

NM_014714.4:c.1246C>T - nonsense - [Sequence Ontology: SO:0001587]

Condition(s)

Name:: Retinitis pigmentosa 80 (RP80)
Identifiers:: MONDO: MONDO:0054708; MedGen: C4540439; OMIM: 617781

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV003841478	3billion	criteria provided, single submitter (ACMG Guidelines, 2015)	Pathogenic (Feb 23, 2023)	unknown	clinical testing	PubMed (2) [See all records that cite these PMIDs] 34890546, 25741868

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV003841478

3billion

criteria provided, single submitter

(ACMG Guidelines, 2015)

Pathogenic
(Feb 23, 2023)

unknown

clinical testing

PubMed (2)
[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	unknown	yes	not provided	not provided	not provided	not provided	not provided	clinical testing

Citations

PubMed

Monoallelic IFT140 pathogenic variants are an important cause of the autosomal dominant polycystic kidney-spectrum phenotype.

Senum SR, Li YSM, Benson KA, Joli G, Olinger E, Lavu S, Madsen CD, Gregory AV, Neatu R, Kline TL, Audrézet MP, Outeda P, Nau CB, Meijer E, Ali H, Steinman TI, Mrug M, Phelan PJ, Watnick TJ, Peters DJM, Ong ACM, Conlon PJ, et al.

Am J Hum Genet. 2022 Jan 6;109(1):136-156. doi: 10.1016/j.ajhg.2021.11.016. Epub 2021 Dec 9.

PubMed [citation]

PMID:: 34890546
PMCID:: PMC8764120

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 3billion, SCV003841478.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (2)

Description

The variant is observed at an extremely low frequency in the gnomAD v2.1.1 dataset (total allele frequency: 0.002%). Stop-gained (nonsense) variant predicted to result in a loss or disruption of normal protein function through nonsense-mediated decay (NMD) or protein truncation. Multiple pathogenic variants are reported downstream of the variant. The variant has been reported to be associated with IFT140-related disorder (PMID: 34890546). Therefore, this variant is classified as Pathogenic according to the recommendation of ACMG/AMP guideline.

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	unknown	yes	not provided	not provided	not provided		not provided	not provided	not provided	not provided

Last Updated: Oct 8, 2024

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