12-21470222-G-A

Variant summary

Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate

The NM_002907.4(RECQL):​c.1922C>T​(p.Ala641Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★★).

Frequency

Genomes: not found (cov: 29)
Exomes 𝑓: 0.0000014 ( 0 hom. )
Failed GnomAD Quality Control

Consequence

RECQL
NM_002907.4 missense

Scores

3
16

Clinical Significance

Uncertain significance criteria provided, multiple submitters, no conflicts U:2

Conservation

PhyloP100: 3.11
Variant links:
Genes affected
RECQL (HGNC:9948): (RecQ like helicase) The protein encoded by this gene is a member of the RecQ DNA helicase family. DNA helicases are enzymes involved in various types of DNA repair, including mismatch repair, nucleotide excision repair and direct repair. The encoded protein is involved in the processing of Holliday junctions, the suppression of sister chromatid exchanges, telomere maintenance, and is required for genotoxic stress resistance. Defects in this gene have been associated with several types of cancer. [provided by RefSeq, Jan 2017]
PYROXD1 (HGNC:26162): (pyridine nucleotide-disulphide oxidoreductase domain 1) This gene encodes a nuclear-cytoplasmic pyridine nucleotide-disulphide reductase (PNDR). PNDRs are flavoproteins that catalyze the pyridine nucleotide-dependent reduction of thiol residues in other proteins. The encoded protein belongs to the class I pyridine nucleotide-disulphide oxidoreductase family but lacks the C-terminal dimerization domain found in other family members and instead has a C-terminal nitrile reductase domain. It localizes to the nucleus and to striated sarcomeric compartments. Naturally occurring mutations in this gene cause early-onset myopathy with internalized nuclei and myofibrillar disorganization. A pseudogene of this gene has been defined on chromosome 11. [provided by RefSeq, Apr 2017]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Uncertain_significance. Variant got 0 ACMG points.

PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (MetaRNN=0.18608606).

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
RECQLNM_002907.4 linkuse as main transcriptc.1922C>T p.Ala641Val missense_variant 15/15 ENST00000444129.7 NP_002898.2
PYROXD1NM_024854.5 linkuse as main transcriptc.*1468G>A 3_prime_UTR_variant 12/12 ENST00000240651.14 NP_079130.2

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
RECQLENST00000444129.7 linkuse as main transcriptc.1922C>T p.Ala641Val missense_variant 15/152 NM_002907.4 ENSP00000416739 P1
RECQLENST00000421138.6 linkuse as main transcriptc.1922C>T p.Ala641Val missense_variant 16/161 ENSP00000395449 P1
PYROXD1ENST00000240651.14 linkuse as main transcriptc.*1468G>A 3_prime_UTR_variant 12/121 NM_024854.5 ENSP00000240651 P1Q8WU10-1
PYROXD1ENST00000538582.5 linkuse as main transcriptc.*1468G>A 3_prime_UTR_variant 12/122 ENSP00000438505 Q8WU10-2

Frequencies

GnomAD3 genomes
Cov.:
29
GnomAD4 exome
Data not reliable, filtered out with message: AS_VQSR
AF:
0.00000137
AC:
2
AN:
1458184
Hom.:
0
Cov.:
38
AF XY:
0.00000138
AC XY:
1
AN XY:
725250
show subpopulations
Gnomad4 AFR exome
AF:
0.00
Gnomad4 AMR exome
AF:
0.00
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.00
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
0.00000180
Gnomad4 OTH exome
AF:
0.00
GnomAD4 genome
Cov.:
29
Bravo
AF:
0.00000378

ClinVar

Significance: Uncertain significance
Submissions summary: Uncertain:2
Revision: criteria provided, multiple submitters, no conflicts
LINK: link

Submissions by phenotype

not specified Uncertain:1
Uncertain significance, criteria provided, single submitterclinical testingAmbry GeneticsFeb 29, 2024The p.A641V variant (also known as c.1922C>T), located in coding exon 14 of the RECQL gene, results from a C to T substitution at nucleotide position 1922. The alanine at codon 641 is replaced by valine, an amino acid with similar properties. This amino acid position is conserved. In addition, this alteration is predicted to be tolerated by in silico analysis. Since supporting evidence is limited at this time, the clinical significance of this alteration remains unclear. -
not provided Uncertain:1
Uncertain significance, criteria provided, single submitterclinical testingLabcorp Genetics (formerly Invitae), LabcorpOct 14, 2019In 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. Algorithms developed to predict the effect of missense changes on protein structure and function (SIFT, PolyPhen-2, Align-GVGD) all suggest that this variant is likely to be tolerated, but these predictions have not been confirmed by published functional studies and their clinical significance is uncertain. This variant has not been reported in the literature in individuals with RECQL-related conditions. This variant is not present in population databases (ExAC no frequency). This sequence change replaces alanine with valine at codon 641 of the RECQL protein (p.Ala641Val). The alanine residue is moderately conserved and there is a small physicochemical difference between alanine and valine. -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
0.091
BayesDel_addAF
Benign
-0.054
T
BayesDel_noAF
Benign
-0.32
CADD
Benign
21
DANN
Uncertain
0.99
DEOGEN2
Benign
0.19
T;T
Eigen
Benign
-0.17
Eigen_PC
Benign
-0.027
FATHMM_MKL
Uncertain
0.90
D
LIST_S2
Benign
0.79
.;T
M_CAP
Benign
0.012
T
MetaRNN
Benign
0.19
T;T
MetaSVM
Benign
-0.88
T
MutationAssessor
Benign
1.8
L;L
MutationTaster
Benign
1.0
D;D;N;N
PrimateAI
Benign
0.39
T
PROVEAN
Benign
-0.41
N;N
REVEL
Benign
0.029
Sift
Uncertain
0.011
D;D
Sift4G
Benign
0.15
T;T
Polyphen
0.041
B;B
Vest4
0.30
MutPred
0.21
Gain of catalytic residue at K637 (P = 0.0055);Gain of catalytic residue at K637 (P = 0.0055);
MVP
0.71
MPC
1.9
ClinPred
0.63
D
GERP RS
3.6
Varity_R
0.064
gMVP
0.061

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.070
Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs1942902579; hg19: chr12-21623156; API