rs121909058
Variant summary
Our verdict is Pathogenic. Variant got 10 ACMG points: 10P and 0B. PM1PM2PP3_StrongPP5_Moderate
The NM_005422.4(TECTA):c.5609A>G(p.Tyr1870Cys) variant causes a missense change involving the alteration of a conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Pathogenic (★).
Frequency
Genomes: not found (cov: 33)
Consequence
TECTA
NM_005422.4 missense
NM_005422.4 missense
Scores
11
5
2
Clinical Significance
Conservation
PhyloP100: 8.91
Genes affected
TECTA (HGNC:11720): (tectorin alpha) The tectorial membrane is an extracellular matrix of the inner ear that contacts the stereocilia bundles of specialized sensory hair cells. Sound induces movement of these hair cells relative to the tectorial membrane, deflects the stereocilia, and leads to fluctuations in hair-cell membrane potential, transducing sound into electrical signals. Alpha-tectorin is one of the major noncollagenous components of the tectorial membrane. Mutations in the TECTA gene have been shown to be responsible for autosomal dominant nonsyndromic hearing impairment and a recessive form of sensorineural pre-lingual non-syndromic deafness. [provided by RefSeq, Jul 2008]
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ACMG classification
Classification made for transcript
Verdict is Pathogenic. Variant got 10 ACMG points.
PM1
?
In a disulfide_bond (size 92) in uniprot entity TECTA_HUMAN there are 13 pathogenic changes around while only 4 benign (76%) in NM_005422.4
PM2
?
Very rare variant in population databases, with high coverage;
PP3
?
MetaRNN computational evidence supports a deleterious effect, 0.966
PP5
?
Variant 11-121168076-A-G is Pathogenic according to our data. Variant chr11-121168076-A-G is described in ClinVar as [Pathogenic]. Clinvar id is 7014.Status of the report is criteria_provided_single_submitter, 1 stars.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TECTA | NM_005422.4 | c.5609A>G | p.Tyr1870Cys | missense_variant | 19/24 | ENST00000392793.6 | |
TBCEL-TECTA | NM_001378761.1 | c.6551A>G | p.Tyr2184Cys | missense_variant | 25/30 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TECTA | ENST00000392793.6 | c.5609A>G | p.Tyr1870Cys | missense_variant | 19/24 | 5 | NM_005422.4 | P4 |
Frequencies
GnomAD3 genomes ? Cov.: 33
GnomAD3 genomes
?
Cov.:
33
GnomAD4 exome Cov.: 31
GnomAD4 exome
Cov.:
31
GnomAD4 genome ? Cov.: 33
GnomAD4 genome
?
Cov.:
33
ClinVar
Significance: Pathogenic
Submissions summary: Pathogenic:2
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
Autosomal dominant nonsyndromic hearing loss 12 Pathogenic:2
Pathogenic, criteria provided, single submitter | research | King Laboratory, University of Washington | Aug 01, 2020 | TECTA c.5609A>G, p.Y1870C is the original mutation responsible for dominantly inherited hearing loss due to TECTA (Nat Genet 1998). The variant alters a residue that is completely conserved in all sequenced vertebrates. It is heterozygous in 2 children with moderate to severe hearing loss from a Palestinian family with dominantly inherited hearing loss documented in 4 generations (Abu Rayyan 2020). The variant is absent from 1300 Palestinian controls and absent from gnomAD v2.1.1. - |
Pathogenic, no assertion criteria provided | literature only | OMIM | May 01, 1998 | - - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Pathogenic
BayesDel_addAF
Pathogenic
D
BayesDel_noAF
Pathogenic
Cadd
Pathogenic
Dann
Uncertain
DEOGEN2
Uncertain
D;.;D
Eigen
Pathogenic
Eigen_PC
Pathogenic
FATHMM_MKL
Pathogenic
D
M_CAP
Uncertain
D
MetaRNN
Pathogenic
D;D;D
MetaSVM
Uncertain
D
MutationAssessor
Uncertain
M;.;M
MutationTaster
Benign
A;A
PrimateAI
Pathogenic
D
PROVEAN
Benign
N;.;N
REVEL
Pathogenic
Sift
Pathogenic
D;.;D
Sift4G
Pathogenic
D;.;D
Polyphen
D;.;D
Vest4
MutPred
Gain of methylation at K1871 (P = 0.0129);.;Gain of methylation at K1871 (P = 0.0129);
MVP
MPC
ClinPred
D
GERP RS
Varity_R
gMVP
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