rs764549158
Variant summary
Our verdict is Uncertain significance. Variant got 4 ACMG points: 4P and 0B. PM2PP3_Moderate
The ENST00000617875.6(RECQL4):c.2419C>T(p.Arg807Cys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000113 in 1,592,090 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 (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R807H) has been classified as Uncertain significance.
Frequency
Consequence
ENST00000617875.6 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
RECQL4 | NM_004260.4 | c.2419C>T | p.Arg807Cys | missense_variant | 14/21 | ENST00000617875.6 | NP_004251.4 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
RECQL4 | ENST00000617875.6 | c.2419C>T | p.Arg807Cys | missense_variant | 14/21 | 1 | NM_004260.4 | ENSP00000482313 | P1 | |
RECQL4 | ENST00000621189.4 | c.1348C>T | p.Arg450Cys | missense_variant | 13/20 | 1 | ENSP00000483145 | |||
ENST00000580385.1 | n.272-344G>A | intron_variant, non_coding_transcript_variant | 3 | |||||||
RECQL4 | ENST00000534626.6 | c.635-124C>T | intron_variant | 5 | ENSP00000477457 |
Frequencies
GnomAD3 genomes AF: 0.0000198 AC: 3AN: 151840Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000138 AC: 3AN: 217598Hom.: 0 AF XY: 0.0000165 AC XY: 2AN XY: 121358
GnomAD4 exome AF: 0.0000104 AC: 15AN: 1440136Hom.: 0 Cov.: 48 AF XY: 0.0000140 AC XY: 10AN XY: 715980
GnomAD4 genome AF: 0.0000197 AC: 3AN: 151954Hom.: 0 Cov.: 33 AF XY: 0.00 AC XY: 0AN XY: 74268
ClinVar
Submissions by phenotype
Baller-Gerold syndrome Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Oct 10, 2023 | This sequence change replaces arginine, which is basic and polar, with cysteine, which is neutral and slightly polar, at codon 807 of the RECQL4 protein (p.Arg807Cys). The frequency data for this variant in the population databases is considered unreliable, as metrics indicate poor data quality at this position in the gnomAD database. This variant has not been reported in the literature in individuals affected with RECQL4-related conditions. ClinVar contains an entry for this variant (Variation ID: 459399). 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 expected to disrupt RECQL4 protein function. In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at