chr17-58572009-TCAGA-T
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Variant summary
Our verdict is Pathogenic. Variant got 12 ACMG points: 12P and 0B. PVS1PM2PP5_Moderate
The NM_031272.5(TEX14):c.3625_3628del(p.Ser1209MetfsTer4) variant causes a frameshift change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000287 in 1,614,030 control chromosomes in the GnomAD database, including 1 homozygotes. Variant has been reported in ClinVar as Pathogenic (★). Variant results in nonsense mediated mRNA decay.
Frequency
Genomes: 𝑓 0.00021 ( 0 hom., cov: 31)
Exomes 𝑓: 0.00030 ( 1 hom. )
Consequence
TEX14
NM_031272.5 frameshift
NM_031272.5 frameshift
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: 1.74
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 17-58572009-TCAGA-T is Pathogenic according to our data. Variant chr17-58572009-TCAGA-T is described in ClinVar as [Pathogenic]. Clinvar id is 1244237.Status of the report is criteria_provided_single_submitter, 1 stars.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
TEX14 | NM_031272.5 | c.3625_3628del | p.Ser1209MetfsTer4 | frameshift_variant | 24/32 | ENST00000349033.10 | NP_112562.3 | |
TEX14 | NM_001201457.2 | c.3763_3766del | p.Ser1255MetfsTer4 | frameshift_variant | 25/33 | NP_001188386.1 | ||
TEX14 | NM_198393.4 | c.3745_3748del | p.Ser1249MetfsTer4 | frameshift_variant | 25/33 | NP_938207.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
TEX14 | ENST00000349033.10 | c.3625_3628del | p.Ser1209MetfsTer4 | frameshift_variant | 24/32 | 5 | NM_031272.5 | ENSP00000268910 | A2 |
Frequencies
GnomAD3 genomes AF: 0.000210 AC: 32AN: 152182Hom.: 0 Cov.: 31
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GnomAD3 exomes AF: 0.000143 AC: 36AN: 251420Hom.: 0 AF XY: 0.000147 AC XY: 20AN XY: 135878
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GnomAD4 exome AF: 0.000296 AC: 432AN: 1461848Hom.: 1 AF XY: 0.000264 AC XY: 192AN XY: 727232
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GnomAD4 genome AF: 0.000210 AC: 32AN: 152182Hom.: 0 Cov.: 31 AF XY: 0.000256 AC XY: 19AN XY: 74350
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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 | - - |
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at