chr17-58573205-TGGTAG-T
Variant summary
Our verdict is Pathogenic. Variant got 12 ACMG points: 12P and 0B. PVS1PM2PP5_Moderate
The NM_031272.5(TEX14):c.3482_3486del(p.Pro1161GlnfsTer19) variant causes a frameshift change. The variant was absent in control chromosomes in GnomAD project. Variant has been reported in ClinVar as Pathogenic (★). Variant results in nonsense mediated mRNA decay.
Frequency
Genomes: not found (cov: 32)
Consequence
TEX14
NM_031272.5 frameshift
NM_031272.5 frameshift
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: 4.53
Genes affected
TEX14 (HGNC:11737): (testis expressed 14, intercellular bridge forming factor) The protein encoded by this gene is necessary for intercellular bridges in germ cells, which are required for spermatogenesis. Three transcript variants encoding different isoforms have been found for this gene.[provided by RefSeq, Jan 2011]
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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 17-58573205-TGGTAG-T is Pathogenic according to our data. Variant chr17-58573205-TGGTAG-T is described in ClinVar as [Pathogenic]. Clinvar id is 1244245.Status of the report is criteria_provided_single_submitter, 1 stars.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TEX14 | NM_031272.5 | c.3482_3486del | p.Pro1161GlnfsTer19 | frameshift_variant | 23/32 | ENST00000349033.10 | |
TEX14 | NM_001201457.2 | c.3620_3624del | p.Pro1207GlnfsTer19 | frameshift_variant | 24/33 | ||
TEX14 | NM_198393.4 | c.3602_3606del | p.Pro1201GlnfsTer19 | frameshift_variant | 24/33 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TEX14 | ENST00000349033.10 | c.3482_3486del | p.Pro1161GlnfsTer19 | frameshift_variant | 23/32 | 5 | NM_031272.5 | A2 |
Frequencies
GnomAD3 genomes ? Cov.: 32
GnomAD3 genomes
?
Cov.:
32
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome ? Cov.: 32
GnomAD4 genome
?
Cov.:
32
ClinVar
Significance: Pathogenic
Submissions summary: Pathogenic:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
Non-obstructive azoospermia Pathogenic:1
Pathogenic, criteria provided, single submitter | research | Institute of Reproductive Genetics, University of Münster | Aug 23, 2021 | - - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
No publications associated with this variant yet.