NM_005333.5:c.569A>G
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_005333.5(HCCS):c.569A>G(p.Lys190Arg) variant causes a missense change. The variant allele was found at a frequency of 0.0000179 in 112,031 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 1 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_005333.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
HCCS | NM_005333.5 | c.569A>G | p.Lys190Arg | missense_variant | Exon 6 of 7 | ENST00000380762.5 | NP_005324.3 | |
HCCS | NM_001122608.3 | c.569A>G | p.Lys190Arg | missense_variant | Exon 6 of 7 | NP_001116080.1 | ||
HCCS | NM_001171991.3 | c.569A>G | p.Lys190Arg | missense_variant | Exon 6 of 7 | NP_001165462.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
HCCS | ENST00000380762.5 | c.569A>G | p.Lys190Arg | missense_variant | Exon 6 of 7 | 1 | NM_005333.5 | ENSP00000370139.4 | ||
HCCS | ENST00000380763.7 | c.569A>G | p.Lys190Arg | missense_variant | Exon 6 of 7 | 1 | ENSP00000370140.3 | |||
HCCS | ENST00000321143.8 | c.569A>G | p.Lys190Arg | missense_variant | Exon 6 of 7 | 2 | ENSP00000326579.4 | |||
ARHGAP6 | ENST00000657361.1 | c.1733-909T>C | intron_variant | Intron 12 of 13 | ENSP00000499351.1 |
Frequencies
GnomAD3 genomes AF: 0.0000179 AC: 2AN: 112031Hom.: 0 Cov.: 24 AF XY: 0.0000292 AC XY: 1AN XY: 34233
GnomAD4 exome Cov.: 29
GnomAD4 genome AF: 0.0000179 AC: 2AN: 112031Hom.: 0 Cov.: 24 AF XY: 0.0000292 AC XY: 1AN XY: 34233
ClinVar
Submissions by phenotype
Inborn genetic diseases Uncertain:1
The c.569A>G (p.K190R) alteration is located in exon 6 (coding exon 5) of the HCCS gene. This alteration results from a A to G substitution at nucleotide position 569, causing the lysine (K) at amino acid position 190 to be replaced by an arginine (R). 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