rs764424917
Variant names:
Your query was ambiguous. Multiple possible variants found:
Variant summary
Our verdict is Uncertain significance. The variant received 2 ACMG points: 2P and 0B. PM2
The NM_005422.4(TECTA):c.2719C>G(p.Arg907Gly) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R907Q) has been classified as Uncertain significance.
Frequency
Genomes: not found (cov: 33)
Consequence
TECTA
NM_005422.4 missense
NM_005422.4 missense
Scores
1
8
10
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 1.08
Publications
3 publications found
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]
TBCEL-TECTA (HGNC:54857): (TBCEL-TECTA readthrough) Predicted to enable alpha-tubulin binding activity. Predicted to be involved in microtubule cytoskeleton organization; post-chaperonin tubulin folding pathway; and tubulin complex assembly. Predicted to be active in cytoplasm. [provided by Alliance of Genome Resources, Apr 2022]
Genome browser will be placed here
ACMG classification
Classification was made for transcript
Our verdict: Uncertain_significance. The variant received 2 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
Transcripts
RefSeq
Ensembl
| Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
|---|---|---|---|---|---|---|---|---|---|---|
| TECTA | ENST00000392793.6 | c.2719C>G | p.Arg907Gly | missense_variant | Exon 10 of 24 | 5 | NM_005422.4 | ENSP00000376543.1 | ||
| TECTA | ENST00000264037.2 | c.2719C>G | p.Arg907Gly | missense_variant | Exon 9 of 23 | 1 | ENSP00000264037.2 | |||
| TECTA | ENST00000642222.1 | c.2719C>G | p.Arg907Gly | missense_variant | Exon 10 of 24 | ENSP00000493855.1 | ||||
| TECTA | ENST00000645008.1 | c.25C>G | p.Arg9Gly | missense_variant | Exon 1 of 15 | ENSP00000496274.1 |
Frequencies
GnomAD3 genomes
GnomAD3 genomes
Cov.:
33
GnomAD4 exome Cov.: 30
GnomAD4 exome
Cov.:
30
GnomAD4 genome
GnomAD4 genome
Cov.:
33
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Pathogenic
BayesDel_addAF
Uncertain
D
BayesDel_noAF
Benign
DANN
Uncertain
DEOGEN2
Benign
T;.;T
Eigen
Benign
Eigen_PC
Benign
FATHMM_MKL
Uncertain
D
LIST_S2
Uncertain
.;D;D
M_CAP
Benign
D
MetaRNN
Uncertain
T;T;T
MetaSVM
Benign
T
MutationAssessor
Benign
N;.;N
PhyloP100
PrimateAI
Benign
T
PROVEAN
Uncertain
N;.;N
REVEL
Uncertain
Sift
Benign
T;.;T
Sift4G
Uncertain
D;.;D
Polyphen
P;.;P
Vest4
MutPred
Gain of ubiquitination at K904 (P = 0.0399);Gain of ubiquitination at K904 (P = 0.0399);Gain of ubiquitination at K904 (P = 0.0399);
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
Publications
You must be logged in to view publications. This limit was set because tens of millions (!) of queries from AI bots are generated daily.