VCV002444130.2 - ClinVar

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

Germline

Classification

The aggregate germline classification for this variant, typically for a monogenic or Mendelian disorder as in the ACMG/AMP guidelines, or for response to a drug. This value is calculated by NCBI based on data from submitters. Read our rules for calculating the aggregate classification.

(2)

Stars represent the aggregate review status, or the level of review supporting the aggregate germline classification for this VCV record. This value is calculated by NCBI based on data from submitters. Read our rules for calculating the review status. The number of submissions which contribute to this review status is shown in parentheses.

Pathogenic

criteria provided, single submitter

Somatic

No data submitted for somatic clinical impact

Somatic

No data submitted for oncogenicity

Variant Details

Identifiers

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

Variation ID: 2444130 Accession: VCV002444130.2

Type and length

single nucleotide variant, 1 bp

Location

Cytogenetic: 16p13.3 16: 1584330 (GRCh38) [ NCBI UCSC ] 16: 1634331 (GRCh37) [ NCBI UCSC ]

Timeline in ClinVar

	First in ClinVar Help The date this variant first appeared in ClinVar with each type of classification.	Last submission Help The date of the most recent submission for each type of classification for this variant.	Last evaluated Help The most recent date that a submitter evaluated this variant for each type of classification.
Germline	Mar 18, 2023	Oct 8, 2024	Feb 23, 2023

HGVS

Nucleotide	Protein	Molecular consequence
NM_014714.4:c.1246C>T MANE Select Help Transcripts from the Matched Annotation from the NCBI and EMBL-EBI (MANE) collaboration.	NP_055529.2:p.Gln416Ter	nonsense
NM_014714.3:c.1246C>T
NC_000016.10:g.1584330G>A
NC_000016.9:g.1634331G>A
NG_032783.1:g.32779C>T

... more HGVS ... less HGVS

Protein change

Q416*

Other names

Canonical SPDI

NC_000016.10:1584329:G:A

Functional consequence Help The effect of the variant on RNA or protein function, based on experimental evidence from submitters.

Global minor allele frequency (GMAF) Help The global minor allele frequency calculated by the 1000 Genomes Project. The minor allele at this location is indicated in parentheses and may be different from the allele represented by this VCV record.

Allele frequency Help The frequency of the allele represented by this VCV record.

Links

VarSome

Genes

Gene	OMIM	ClinGen Gene Dosage Sensitivity Curation		Variation Viewer Help Links to Variation Viewer, a genome browser to view variation data from NCBI databases.	Related variants
Gene	OMIM	HI score Help The haploinsufficiency score for the gene, curated by ClinGen’s Dosage Sensitivity Curation task team.	TS score Help The triplosensitivity score for the gene, curated by ClinGen’s Dosage Sensitivity Curation task team.		Within gene Help The number of variants in ClinVar that are contained within this gene, with a link to view the list of variants.	All Help The number of variants in ClinVar for this gene, including smaller variants within the gene and larger CNVs that overlap or fully contain the gene.
IFT140		-	-	GRCh38 GRCh37	1064	1921
LOC105371046	-	-	-	GRCh38	-	616

Conditions - Germline

Condition Help The condition for this variant-condition (RCV) record in ClinVar.	Classification Help The aggregate germline classification for this variant-condition (RCV) record in ClinVar. The number of submissions that contribute to this aggregate classification is shown in parentheses. (# of submissions)	Review status Help The aggregate review status for this variant-condition (RCV) record in ClinVar. This value is calculated by NCBI based on data from submitters. Read our rules for calculating the review status.	Last evaluated Help The most recent date that a submitter evaluated this variant for the condition.	Variation/condition record Help The RCV accession number, with most recent version number, for the variant-condition record, with a link to the RCV web page.
Retinitis pigmentosa 80	Pathogenic (1)	criteria provided, single submitter	Feb 23, 2023	RCV003152928.1
IFT140-related disorder	Pathogenic (1)	no assertion criteria provided	Apr 18, 2024	RCV004731512.1

Submissions - Germline

Classification Help The submitted germline classification for each SCV record. (Last evaluated)	Review status Help Stars represent the review status, or the level of review supporting the submitted (SCV) record. This value is calculated by NCBI based on data from the submitter. Read our rules for calculating the review status. This column also includes a link to the submitter’s assertion criteria if provided, and the collection method. (Assertion criteria)	Condition Help The condition for the classification, provided by the submitter for this submitted (SCV) record. This column also includes the affected status and allele origin of individuals observed with this variant.	Submitter Help The submitting organization for this submitted (SCV) record. This column also includes the SCV accession and version number, the date this SCV first appeared in ClinVar, and the date that this SCV was last updated in ClinVar.	More information Help This column includes more information supporting the classification, including citations, the comment on classification, and detailed evidence provided as observations of the variant by the submitter.
Pathogenic (Feb 23, 2023)	criteria provided, single submitter (ACMG Guidelines, 2015) Method: clinical testing	Retinitis pigmentosa 80 Affected status: yes Allele origin: unknown	3billion Accession: SCV003841478.1 First in ClinVar: Mar 18, 2023 Last updated: Mar 18, 2023	Publications: PubMed (1) PubMed: 34890546 Comment: 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 … (more) 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. (less) Clinical Features: Visual impairment (present) , Strabismus (present) , Optic disc pallor (present) , Headache (present)
Pathogenic (Apr 18, 2024)	no assertion criteria provided Method: clinical testing	IFT140-related condition Affected status: unknown Allele origin: germline	PreventionGenetics, part of Exact Sciences Accession: SCV005336885.1 First in ClinVar: Oct 08, 2024 Last updated: Oct 08, 2024	Comment: The IFT140 c.1246C>T variant is predicted to result in premature protein termination (p.Gln416). This variant was reported in an individual with the autosomal dominant polycystic … (more) The IFT140 c.1246C>T variant is predicted to result in premature protein termination (p.Gln416). This variant was reported in an individual with the autosomal dominant polycystic kidney-spectrum phenotype (Senum et al. 2022. PubMed ID: 34890546). This variant is reported in 0.020% of alleles in individuals of South Asian descent in gnomAD. Nonsense variants in IFT140 are expected to be pathogenic. This variant is interpreted as pathogenic for both autosomal dominant and autosomal recessive IFT140-related disorders. (less)

Comment:

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.

Comment:

The IFT140 c.1246C>T variant is predicted to result in premature protein termination (p.Gln416*). This variant was reported in an individual with the autosomal dominant polycystic kidney-spectrum phenotype (Senum et al. 2022. PubMed ID: 34890546). This variant is reported in 0.020% of alleles in individuals of South Asian descent in gnomAD. Nonsense variants in IFT140 are expected to be pathogenic. This variant is interpreted as pathogenic for both autosomal dominant and autosomal recessive IFT140-related disorders.

Germline Functional Evidence

There is no functional evidence in ClinVar for this variation. If you have generated functional data for this variation, please consider submitting that data to ClinVar.

Comment:

Citations for germline classification of this variant

Title	Author	Journal	Year	Link
Monoallelic IFT140 pathogenic variants are an important cause of the autosomal dominant polycystic kidney-spectrum phenotype.	Senum SR	American journal of human genetics	2022	PMID: 34890546

Text-mined citations for this variant ...

Record last updated Oct 08, 2024

ClinVar Genomic variation as it relates to human health

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

Variant Details

Genes

Conditions - Germline

Submissions - Germline

Germline Functional Evidence

Citations for germline classification of this variant

Text-mined citations for this variant ...