18-46435323-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_152470.3(ARK2C):c.412C>T(p.Arg138Cys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000041 in 1,461,870 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_152470.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
ARK2C | NM_152470.3 | c.412C>T | p.Arg138Cys | missense_variant | Exon 3 of 8 | ENST00000269439.12 | NP_689683.2 | |
ARK2C | XM_011526016.4 | c.412C>T | p.Arg138Cys | missense_variant | Exon 3 of 7 | XP_011524318.1 | ||
ARK2C | XM_017025788.3 | c.412C>T | p.Arg138Cys | missense_variant | Exon 3 of 4 | XP_016881277.1 | ||
ARK2C | NM_001256758.1 | c.-91-12240C>T | intron_variant | Intron 1 of 5 | NP_001243687.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
RNF165 | ENST00000269439.12 | c.412C>T | p.Arg138Cys | missense_variant | Exon 3 of 8 | 2 | NM_152470.3 | ENSP00000269439.6 | ||
RNF165 | ENST00000593230.5 | c.211C>T | p.Arg71Cys | missense_variant | Exon 3 of 5 | 3 | ENSP00000467730.1 | |||
RNF165 | ENST00000543885.2 | c.-91-12240C>T | intron_variant | Intron 1 of 5 | 2 | ENSP00000444285.1 | ||||
RNF165 | ENST00000586604.5 | n.62-12240C>T | intron_variant | Intron 1 of 5 | 2 | ENSP00000468365.1 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD3 exomes AF: 0.00000398 AC: 1AN: 251454Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 135904
GnomAD4 exome AF: 0.00000410 AC: 6AN: 1461870Hom.: 0 Cov.: 31 AF XY: 0.00000550 AC XY: 4AN XY: 727240
GnomAD4 genome Cov.: 32
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.412C>T (p.R138C) alteration is located in exon 3 (coding exon 3) of the RNF165 gene. This alteration results from a C to T substitution at nucleotide position 412, causing the arginine (R) at amino acid position 138 to be replaced by a cysteine (C). 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