rs1553506928
Positions:
Variant summary
Our verdict is Pathogenic. Variant got 10 ACMG points: 10P and 0B. PVS1PM2
The NM_024753.5(TTC21B):c.3025_3026insATTTT(p.Phe1009TyrfsTer57) variant causes a frameshift change. The variant allele was found at a frequency of 0.0000089 in 1,461,190 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (★). Variant results in nonsense mediated mRNA decay.
Frequency
Genomes: not found (cov: 32)
Exomes 𝑓: 0.0000089 ( 0 hom. )
Consequence
TTC21B
NM_024753.5 frameshift
NM_024753.5 frameshift
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: 5.60
Genes affected
TTC21B (HGNC:25660): (tetratricopeptide repeat domain 21B) This gene encodes a member of TTC21 family, containing several tetratricopeptide repeat (TPR) domains. This protein is localized to the cilium axoneme, and may play a role in retrograde intraflagellar transport in cilia. Mutations in this gene are associated with various ciliopathies, nephronophthisis 12, and asphyxiating thoracic dystrophy 4. [provided by RefSeq, Oct 2011]
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ACMG classification
Classification made for transcript
Verdict is Pathogenic. Variant got 10 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;
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TTC21B | NM_024753.5 | c.3025_3026insATTTT | p.Phe1009TyrfsTer57 | frameshift_variant | 23/29 | ENST00000243344.8 | |
TTC21B | XM_011511871.4 | c.2275_2276insATTTT | p.Phe759TyrfsTer57 | frameshift_variant | 18/24 | ||
TTC21B | XM_017004967.2 | c.3025_3026insATTTT | p.Phe1009TyrfsTer57 | frameshift_variant | 23/28 | ||
TTC21B | XM_047445870.1 | c.2371_2372insATTTT | p.Phe791TyrfsTer57 | frameshift_variant | 19/25 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TTC21B | ENST00000243344.8 | c.3025_3026insATTTT | p.Phe1009TyrfsTer57 | frameshift_variant | 23/29 | 1 | NM_024753.5 | P1 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD3 genomes
Cov.:
32
GnomAD4 exome AF: 0.00000890 AC: 13AN: 1461190Hom.: 0 Cov.: 31 AF XY: 0.0000124 AC XY: 9AN XY: 726886
GnomAD4 exome
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13
AN:
1461190
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31
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9
AN XY:
726886
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GnomAD4 genome Cov.: 32
GnomAD4 genome
Cov.:
32
ClinVar
Significance: Uncertain significance
Submissions summary: Uncertain:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Genetic Services Laboratory, University of Chicago | Sep 26, 2016 | - - |
Computational scores
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Name
Calibrated prediction
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Prediction
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at