16-1587222-A-G
Variant summary
Our verdict is Likely pathogenic. Variant got 7 ACMG points: 7P and 0B. PM1PM2PP3_ModeratePP5
The NM_014714.4(IFT140):āc.985T>Cā(p.Cys329Arg) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.00000186 in 1,610,208 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 Pathogenic (no stars). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. C329Y) has been classified as Uncertain significance.
Frequency
Consequence
NM_014714.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_pathogenic. Variant got 7 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
IFT140 | NM_014714.4 | c.985T>C | p.Cys329Arg | missense_variant | 9/31 | ENST00000426508.7 | |
LOC105371046 | NR_135176.1 | n.59+6637A>G | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
IFT140 | ENST00000426508.7 | c.985T>C | p.Cys329Arg | missense_variant | 9/31 | 5 | NM_014714.4 | P1 | |
ENST00000563162.1 | n.59+6637A>G | intron_variant, non_coding_transcript_variant | 2 | ||||||
IFT140 | ENST00000439987.6 | n.1046T>C | non_coding_transcript_exon_variant | 8/19 | 2 | ||||
IFT140 | ENST00000397417.6 | c.329-2802T>C | intron_variant, NMD_transcript_variant | 5 |
Frequencies
GnomAD3 genomes AF: 0.0000131 AC: 2AN: 152190Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.00000796 AC: 2AN: 251408Hom.: 0 AF XY: 0.00000736 AC XY: 1AN XY: 135904
GnomAD4 exome AF: 6.86e-7 AC: 1AN: 1458018Hom.: 0 Cov.: 28 AF XY: 0.00000138 AC XY: 1AN XY: 725696
GnomAD4 genome AF: 0.0000131 AC: 2AN: 152190Hom.: 0 Cov.: 32 AF XY: 0.0000134 AC XY: 1AN XY: 74358
ClinVar
Submissions by phenotype
Retinitis pigmentosa 80 Pathogenic:1
Pathogenic, no assertion criteria provided | literature only | OMIM | Nov 22, 2017 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at