17-15314119-GC-CA

Variant names:

• chr17-15314119-GC-CA
• NM_031898.3:c.845_846delGCinsTG
• TEKT3 p.Gly282Val

Variant summary

Our verdict is Uncertain significance. The variant received 1 ACMG points: 1P and 0B. PP2

The NM_031898.3(TEKT3):​c.845_846delGCinsTG​(p.Gly282Val) variant causes a missense change. 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 MNV, and the frequency of such variant types in population databases may be underestimated and unreliable. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: not found (cov: 33)
• Consequence: TEKT3 NM_031898.3 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 5.86
• Publications: 0 publications found

Genes affected

TEKT3 (HGNC:14293): (tektin 3) This gene product belongs to the tektin family of proteins. Tektins comprise a family of filament-forming proteins that are coassembled with tubulins to form ciliary and flagellar microtubules. The exact function of this gene is not known. [provided by RefSeq, Jul 2008]

TEKT3 Gene-Disease associations (from GenCC):

• spermatogenic failure 81

  Inheritance: Unknown Classification: LIMITED Submitted by: Labcorp Genetics (formerly Invitae)

ACMG classification

Our verdict: Uncertain_significance. The variant received 1 ACMG points.

• PP2: Missense variant in the gene, where a lot of missense mutations are associated with disease in ClinVar. The gene has 2 curated pathogenic missense variants (we use a threshold of 10). The gene has 0 curated benign missense variants. Gene score misZ: 0.20346 (below the threshold of 3.09). Trascript score misZ: 0.91588 (below the threshold of 3.09). GenCC associations: The gene is linked to spermatogenic failure 81.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_031898.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TEKT3	NM_031898.3	MANE Select	c.845_846delGCinsTG	p.Gly282Val	missense	N/A	NP_114104.1	Q9BXF9

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TEKT3	ENST00000395930.6	TSL:1 MANE Select	c.845_846delGCinsTG	p.Gly282Val	missense	N/A	ENSP00000379263.1	Q9BXF9
	TEKT3	ENST00000338696.6	TSL:1	c.845_846delGCinsTG	p.Gly282Val	missense	N/A	ENSP00000343995.2	Q9BXF9
	TEKT3	ENST00000539245.5	TSL:5	c.347_348delGCinsTG	p.Gly116Val	missense	N/A	ENSP00000443280.1	F5H5M8

Frequencies

GnomAD3 genomes Cov.: 33

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

GnomAD4 genome Cov.: 33

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
PhyloP100		5.9

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

hg19: chr17-15217436;