10-62199846-C-T
Variant summary
Our verdict is Likely pathogenic. Variant got 6 ACMG points: 6P and 0B. PM2PP3_Strong
The NM_145307.4(RTKN2):c.1202G>A(p.Cys401Tyr) variant causes a missense change. The variant allele was found at a frequency of 0.0000124 in 1,611,306 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 Uncertain significance (★).
Frequency
Consequence
NM_145307.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_pathogenic. Variant got 6 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
RTKN2 | ENST00000373789.8 | c.1202G>A | p.Cys401Tyr | missense_variant | Exon 11 of 12 | 1 | NM_145307.4 | ENSP00000362894.3 | ||
RTKN2 | ENST00000315289.6 | c.608G>A | p.Cys203Tyr | missense_variant | Exon 7 of 9 | 2 | ENSP00000325379.2 |
Frequencies
GnomAD3 genomes AF: 0.00000657 AC: 1AN: 152154Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.00000796 AC: 2AN: 251116Hom.: 0 AF XY: 0.0000147 AC XY: 2AN XY: 135738
GnomAD4 exome AF: 0.0000130 AC: 19AN: 1459152Hom.: 0 Cov.: 28 AF XY: 0.0000138 AC XY: 10AN XY: 726024
GnomAD4 genome AF: 0.00000657 AC: 1AN: 152154Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 74320
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.1202G>A (p.C401Y) alteration is located in exon 11 (coding exon 11) of the RTKN2 gene. This alteration results from a G to A substitution at nucleotide position 1202, causing the cysteine (C) at amino acid position 401 to be replaced by a tyrosine (Y). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at