rs758052634
Variant summary
Our verdict is Pathogenic. Variant got 11 ACMG points: 11P and 0B. PM2PP3PP5_Very_Strong
The NM_014714.4(IFT140):c.1451C>T(p.Thr484Met) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.0000124 in 1,613,176 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Likely pathogenic (★★). Synonymous variant affecting the same amino acid position (i.e. T484T) has been classified as Likely benign.
Frequency
Consequence
NM_014714.4 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Pathogenic. Variant got 11 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
IFT140 | NM_014714.4 | c.1451C>T | p.Thr484Met | missense_variant | 13/31 | ENST00000426508.7 | |
LOC105371046 | NR_135176.1 | n.59+247G>A | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
IFT140 | ENST00000426508.7 | c.1451C>T | p.Thr484Met | missense_variant | 13/31 | 5 | NM_014714.4 | P1 | |
ENST00000563162.1 | n.59+247G>A | intron_variant, non_coding_transcript_variant | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.0000131 AC: 2AN: 152182Hom.: 0 Cov.: 31
GnomAD3 exomes AF: 0.0000318 AC: 8AN: 251284Hom.: 0 AF XY: 0.0000589 AC XY: 8AN XY: 135848
GnomAD4 exome AF: 0.0000123 AC: 18AN: 1460994Hom.: 0 Cov.: 29 AF XY: 0.0000165 AC XY: 12AN XY: 726830
GnomAD4 genome ? AF: 0.0000131 AC: 2AN: 152182Hom.: 0 Cov.: 31 AF XY: 0.0000269 AC XY: 2AN XY: 74354
ClinVar
Submissions by phenotype
Retinitis pigmentosa 80 Pathogenic:1
Pathogenic, no assertion criteria provided | literature only | OMIM | Feb 08, 2024 | - - |
Saldino-Mainzer syndrome;C4540439:Retinitis pigmentosa 80 Pathogenic:1
Likely pathogenic, criteria provided, single submitter | clinical testing | Fulgent Genetics, Fulgent Genetics | Aug 23, 2021 | - - |
not provided Pathogenic:1
Pathogenic, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Aug 01, 2023 | IFT140: PM3:Very Strong, PM2, PP1, PS3:Supporting, BP4 - |
Saldino-Mainzer syndrome Pathogenic:1
Pathogenic, criteria provided, single submitter | clinical testing | Invitae | Jul 07, 2023 | This sequence change replaces threonine, which is neutral and polar, with methionine, which is neutral and non-polar, at codon 484 of the IFT140 protein (p.Thr484Met). For these reasons, this variant has been classified as Pathogenic. Experimental studies have shown that this missense change affects IFT140 function (PMID: 26968735). Advanced modeling of protein sequence and biophysical properties (such as structural, functional, and spatial information, amino acid conservation, physicochemical variation, residue mobility, and thermodynamic stability) performed at Invitae indicates that this missense variant is not expected to disrupt IFT140 protein function. ClinVar contains an entry for this variant (Variation ID: 446314). This missense change has been observed in individuals with retinal dystrophy (PMID: 26216056, 26968735, 31736247). It has also been observed to segregate with disease in related individuals. This variant is present in population databases (rs758052634, gnomAD 0.02%). - |
Retinal dystrophy Pathogenic:1
Pathogenic, criteria provided, single submitter | clinical testing | Blueprint Genetics | Nov 08, 2018 | - - |
Retinitis pigmentosa Pathogenic:1
Pathogenic, criteria provided, single submitter | clinical testing | Women's Health and Genetics/Laboratory Corporation of America, LabCorp | Jul 27, 2022 | Variant summary: IFT140 c.1451C>T (p.Thr484Met) results in a non-conservative amino acid change in the encoded protein sequence. Four of five in-silico tools predict a damaging effect of the variant on protein function. The variant allele was found at a frequency of 3.2e-05 in 251284 control chromosomes (gnomAD). The variant, c.1451C>T, has been reported in the literature in multiple homozygous and compound heterozygous individuals affected with retinal dystrophy (Hull_2016, Xu_2015, Zenteno_2020), and in one of the reported families the variant segregated with disease (Hull_2016). These data indicate that the variant is very likely to be associated with disease. One of these publications also reported experimental evidence evaluating an impact on protein function, and demonstrated subcellular mislocalization for the variant protein (Hull_2016). Three submitters have provided clinical-significance assessments for this variant in ClinVar after 2014, and all classified the variant as pathogenic. Based on the evidence outlined above, the variant was classified as pathogenic. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at