rs1555568575

Variant names:

• chr17-58587937-CTGCCGGTGGCT-C
• rs1555568575
• NM_031272.5:c.2650_2660delAGCCACCGGCA

Variant summary

Our verdict is Likely pathogenic. The variant received 9 ACMG points: 9P and 0B. PVS1 PP5

The NM_031272.5(TEX14):​c.2650_2660delAGCCACCGGCA​(p.Ser884GlyfsTer23) variant causes a frameshift change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. It is difficult to determine the true allele frequency of this variant because it is of type DEL_BIG, and the frequency of such variant types in population databases may be underestimated and unreliable. Variant has been reported in ClinVar as Pathogenic (no stars). Variant results in nonsense mediated mRNA decay.

• Frequency: Genomes: not found (cov: 31)
• Consequence: TEX14 NM_031272.5 frameshift
• Clinical Significance: Pathogenic no assertion criteria provided P:1
• Conservation: PhyloP100: 2.25
• Publications: 0 publications found

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]

TEX14 Gene-Disease associations (from GenCC):

• male infertility with azoospermia or oligozoospermia due to single gene mutation

  Inheritance: AD Classification: SUPPORTIVE Submitted by: Orphanet

ACMG classification

Our verdict: Likely_pathogenic. The variant received 9 ACMG points.

• PVS1: Loss of function variant, product undergoes nonsense mediated mRNA decay. LoF is a known mechanism of disease.
• PP5: Variant 17-58587937-CTGCCGGTGGCT-C is Pathogenic according to our data. Variant chr17-58587937-CTGCCGGTGGCT-C is described in ClinVar as Pathogenic. ClinVar VariationId is 440758.Status of the report is no_assertion_criteria_provided, 0 stars.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TEX14	NM_031272.5	c.2650_2660delAGCCACCGGCA	p.Ser884GlyfsTer23	frameshift_variant	Exon 16 of 32	ENST00000349033.10	NP_112562.3
TEX14	NM_001201457.2	c.2668_2678delAGCCACCGGCA	p.Ser890GlyfsTer23	frameshift_variant	Exon 16 of 33		NP_001188386.1
TEX14	NM_198393.4	c.2650_2660delAGCCACCGGCA	p.Ser884GlyfsTer23	frameshift_variant	Exon 16 of 33		NP_938207.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
TEX14	ENST00000349033.10	c.2650_2660delAGCCACCGGCA	p.Ser884GlyfsTer23	frameshift_variant	Exon 16 of 32	5	NM_031272.5	ENSP00000268910.8

Frequencies

GnomAD3 genomes Cov.: 31

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome Cov.: 31

ClinVar

Significance: Pathogenic

Submissions summary: Pathogenic:1

Revision: no assertion criteria provided

Submissions by phenotype

Spermatogenic failure 23 Pathogenic:1

Jun 28, 2019

OMIM

Significance: Pathogenic

Review Status: no assertion criteria provided

Collection Method: literature only

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Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
PhyloP100		2.3
Mutation Taster		=4/196	disease causing (ClinVar)

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs1555568575; hg19: chr17-56665298;