12-21470207-ATTTTTC-A
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM4
The NM_002907.4(RECQL):c.1931_1936delGAAAAA(p.Arg644_Lys645del) variant causes a disruptive inframe deletion change. Variant has been reported in ClinVar as Uncertain significance (★★).
Frequency
Consequence
NM_002907.4 disruptive_inframe_deletion
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 |
---|---|---|---|---|---|---|---|---|
RECQL | NM_002907.4 | c.1931_1936delGAAAAA | p.Arg644_Lys645del | disruptive_inframe_deletion | Exon 15 of 15 | ENST00000444129.7 | NP_002898.2 | |
PYROXD1 | NM_024854.5 | c.*1458_*1463delTCTTTT | 3_prime_UTR_variant | Exon 12 of 12 | ENST00000240651.14 | NP_079130.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
RECQL | ENST00000444129.7 | c.1931_1936delGAAAAA | p.Arg644_Lys645del | disruptive_inframe_deletion | Exon 15 of 15 | 2 | NM_002907.4 | ENSP00000416739.2 | ||
RECQL | ENST00000421138.6 | c.1931_1936delGAAAAA | p.Arg644_Lys645del | disruptive_inframe_deletion | Exon 16 of 16 | 1 | ENSP00000395449.2 | |||
PYROXD1 | ENST00000240651.14 | c.*1458_*1463delTCTTTT | 3_prime_UTR_variant | Exon 12 of 12 | 1 | NM_024854.5 | ENSP00000240651.9 | |||
PYROXD1 | ENST00000538582.5 | c.*1458_*1463delTCTTTT | 3_prime_UTR_variant | Exon 12 of 12 | 2 | ENSP00000438505.1 |
Frequencies
GnomAD3 genomes AF: 0.00 AC: 2AN: 151654Hom.: 0 Cov.: 29 FAILED QC
GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 6.85e-7 AC: 1AN: 1459838Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 726226
GnomAD4 genome Data not reliable, filtered out with message: AS_VQSR AF: 0.0000132 AC: 2AN: 151654Hom.: 0 Cov.: 29 AF XY: 0.00 AC XY: 0AN XY: 74042
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.1931_1936delGAAAAA variant (also known as p.R644_K645del) is located in coding exon 14 of the RECQL gene. This variant results from an in-frame GAAAAA deletion at nucleotide positions 1931 to 1936. This results in the in-frame deletion of two amino acids (RK) at codons 644 to 645. The deleted amino acid positions are highly conserved in available vertebrate species. In addition, this alteration is predicted to be neutral by in silico analysis (Choi Y et al. PLoS ONE. 2012; 7(10):e46688). The evidence for this gene-disease relationship is limited; therefore, the clinical significance of this alteration is unclear. -
not provided Uncertain:1
In-frame deletion of 2 amino acids in a non-repeat region; Not observed at a significant frequency in large population cohorts (Lek 2016); Has not been previously published as pathogenic or benign to our knowledge; In silico analysis, which includes protein predictors and evolutionary conservation, supports that this variant does not alter protein structure/function -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at