NM_004260.4:c.3613C>T
Variant names:
Variant summary
Our verdict is Uncertain significance. The variant received 4 ACMG points: 4P and 0B. PVS1_ModeratePM2
The NM_004260.4(RECQL4):c.3613C>T(p.Gln1205*) variant causes a stop gained change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000959 in 1,460,130 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 (★). Synonymous variant affecting the same amino acid position (i.e. Q1205Q) has been classified as Likely benign.
Frequency
Genomes: not found (cov: 34)
Exomes 𝑓: 0.0000096 ( 0 hom. )
Consequence
RECQL4
NM_004260.4 stop_gained
NM_004260.4 stop_gained
Scores
2
1
1
Clinical Significance
Conservation
PhyloP100: 0.790
Publications
1 publications found
Genes affected
RECQL4 (HGNC:9949): (RecQ like helicase 4) The protein encoded by this gene is a DNA helicase that belongs to the RecQ helicase family. DNA helicases unwind double-stranded DNA into single-stranded DNAs and may modulate chromosome segregation. This gene is predominantly expressed in thymus and testis. Mutations in this gene are associated with Rothmund-Thomson, RAPADILINO and Baller-Gerold syndromes. [provided by RefSeq, Jan 2010]
SLC33A2 (HGNC:25157): (major facilitator superfamily domain containing 3) Predicted to enable solute:proton symporter activity. Predicted to be involved in proton transmembrane transport. Predicted to be integral component of membrane. [provided by Alliance of Genome Resources, Apr 2022]
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ACMG classification
Classification was made for transcript
Our verdict: Uncertain_significance. The variant received 4 ACMG points.
PVS1
Loss of function variant, product does not undergo nonsense mediated mRNA decay. Variant is located in the 3'-most exon, not predicted to undergo nonsense mediated mRNA decay. Fraction of 0.00386 CDS is truncated, and there are 0 pathogenic variants in the truncated region.
PM2
Very rare variant in population databases, with high coverage;
Variant Effect in Transcripts
ACMG analysis was done for transcript: NM_004260.4. You can select a different transcript below to see updated ACMG assignments.
RefSeq Transcripts
| Sel. | Gene | Transcript | Tags | HGVSc | HGVSp | Effect | Exon Rank | Protein | UniProt |
|---|---|---|---|---|---|---|---|---|---|
| RECQL4 | NM_004260.4 | MANE Select | c.3613C>T | p.Gln1205* | stop_gained | Exon 21 of 21 | NP_004251.4 | O94761 | |
| RECQL4 | NM_001413019.1 | c.3688C>T | p.Gln1230* | stop_gained | Exon 20 of 20 | NP_001399948.1 | |||
| RECQL4 | NM_001413036.1 | c.3622C>T | p.Gln1208* | stop_gained | Exon 21 of 21 | NP_001399965.1 |
Ensembl Transcripts
| Sel. | Gene | Transcript | Tags | HGVSc | HGVSp | Effect | Exon Rank | Protein | UniProt |
|---|---|---|---|---|---|---|---|---|---|
| RECQL4 | ENST00000617875.6 | TSL:1 MANE Select | c.3613C>T | p.Gln1205* | stop_gained | Exon 21 of 21 | ENSP00000482313.2 | O94761 | |
| RECQL4 | ENST00000621189.4 | TSL:1 | c.2542C>T | p.Gln848* | stop_gained | Exon 20 of 20 | ENSP00000483145.1 | A0A087X072 | |
| RECQL4 | ENST00000971710.1 | c.3520C>T | p.Gln1174* | stop_gained | Exon 21 of 21 | ENSP00000641769.1 |
Frequencies
GnomAD3 genomes
GnomAD3 genomes
Cov.:
34
GnomAD2 exomes AF: 0.0000242 AC: 6AN: 247932 AF XY: 0.0000222 show subpopulations
GnomAD2 exomes
AF:
AC:
6
AN:
247932
AF XY:
Gnomad AFR exome
AF:
Gnomad AMR exome
AF:
Gnomad ASJ exome
AF:
Gnomad EAS exome
AF:
Gnomad FIN exome
AF:
Gnomad NFE exome
AF:
Gnomad OTH exome
AF:
GnomAD4 exome AF: 0.00000959 AC: 14AN: 1460130Hom.: 0 Cov.: 33 AF XY: 0.0000124 AC XY: 9AN XY: 726304 show subpopulations
GnomAD4 exome
AF:
AC:
14
AN:
1460130
Hom.:
Cov.:
33
AF XY:
AC XY:
9
AN XY:
726304
show subpopulations
African (AFR)
AF:
AC:
0
AN:
33478
American (AMR)
AF:
AC:
0
AN:
44716
Ashkenazi Jewish (ASJ)
AF:
AC:
0
AN:
26134
East Asian (EAS)
AF:
AC:
0
AN:
39692
South Asian (SAS)
AF:
AC:
8
AN:
86258
European-Finnish (FIN)
AF:
AC:
0
AN:
52068
Middle Eastern (MID)
AF:
AC:
0
AN:
5766
European-Non Finnish (NFE)
AF:
AC:
5
AN:
1111672
Other (OTH)
AF:
AC:
1
AN:
60346
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.500
Heterozygous variant carriers
0
1
2
4
5
6
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
GnomAD4 genome
GnomAD4 genome
Cov.:
34
ExAC
AF:
AC:
5
ClinVar
ClinVar submissions
View on ClinVar Significance:Uncertain significance
Revision:criteria provided, single submitter
Pathogenic
VUS
Benign
Condition
-
1
-
Baller-Gerold syndrome (1)
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_addAF
Pathogenic
D
BayesDel_noAF
Pathogenic
DANN
Benign
FATHMM_MKL
Uncertain
D
PhyloP100
Vest4
GERP RS
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
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