rs201956469
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Variant summary
Our verdict is Pathogenic. Variant got 12 ACMG points: 12P and 0B. PVS1PM2PP5_Moderate
The NM_017799.4(TMEM260):c.1393C>T(p.Gln465Ter) variant causes a stop gained change. The variant allele was found at a frequency of 0.0000417 in 1,604,896 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 Pathogenic (★). Variant results in nonsense mediated mRNA decay.
Frequency
Genomes: 𝑓 0.000053 ( 0 hom., cov: 31)
Exomes 𝑓: 0.000041 ( 0 hom. )
Consequence
TMEM260
NM_017799.4 stop_gained
NM_017799.4 stop_gained
Scores
5
1
1
Clinical Significance
Conservation
PhyloP100: 6.93
Genes affected
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ACMG classification
Classification made for transcript
Verdict is Pathogenic. Variant got 12 ACMG points.
PVS1
?
Loss of function variant, product undergoes nonsense mediated mRNA decay. LoF is a known mechanism of disease.
PM2
?
Very rare variant in population databases, with high coverage;
PP5
?
Variant 14-56621697-C-T is Pathogenic according to our data. Variant chr14-56621697-C-T is described in ClinVar as [Pathogenic]. Clinvar id is 426075.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr14-56621697-C-T is described in Lovd as [Pathogenic].
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TMEM260 | NM_017799.4 | c.1393C>T | p.Gln465Ter | stop_gained | 11/16 | ENST00000261556.11 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TMEM260 | ENST00000261556.11 | c.1393C>T | p.Gln465Ter | stop_gained | 11/16 | 2 | NM_017799.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000526 AC: 8AN: 152006Hom.: 0 Cov.: 31
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GnomAD3 exomes AF: 0.0000743 AC: 18AN: 242376Hom.: 0 AF XY: 0.0000841 AC XY: 11AN XY: 130748
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GnomAD4 exome AF: 0.0000406 AC: 59AN: 1452890Hom.: 0 Cov.: 30 AF XY: 0.0000429 AC XY: 31AN XY: 722402
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GnomAD4 genome ? AF: 0.0000526 AC: 8AN: 152006Hom.: 0 Cov.: 31 AF XY: 0.0000539 AC XY: 4AN XY: 74232
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ClinVar
Significance: Pathogenic
Submissions summary: Pathogenic:2
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
Structural heart defects and renal anomalies syndrome Pathogenic:1
Pathogenic, no assertion criteria provided | literature only | OMIM | Nov 05, 2021 | - - |
not provided Pathogenic:1
Pathogenic, criteria provided, single submitter | clinical testing | Invitae | Sep 02, 2021 | - - |
Computational scores
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Name
Calibrated prediction
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Prediction
BayesDel_addAF
Pathogenic
D
BayesDel_noAF
Pathogenic
CADD
Pathogenic
DANN
Uncertain
Eigen
Pathogenic
Eigen_PC
Pathogenic
FATHMM_MKL
Pathogenic
D
MutationTaster
Benign
A;D;D
Vest4
GERP RS
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at