NM_024809.5:c.254_255delTG

Variant names:

• chr12-123672116-CTG-C
• rs786205622
• NM_024809.5:c.254_255delTG

Variant summary

Our verdict is Pathogenic. The variant received 12 ACMG points: 12P and 0B. PVS1 PM2 PP5_Moderate

The NM_024809.5(TCTN2):​c.254_255delTG​(p.Val85AspfsTer24) variant causes a frameshift change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. Variant has been reported in ClinVar as Likely pathogenic (★). Synonymous variant affecting the same amino acid position (i.e. V85V) has been classified as Likely benign. Variant results in nonsense mediated mRNA decay.

• Frequency: Genomes: not found (cov: 32)
• Consequence: TCTN2 NM_024809.5 frameshift
• Clinical Significance: Likely pathogenic criteria provided, single submitter P:1
• Conservation: PhyloP100: 2.11
• Publications: 2 publications found

Genes affected

TCTN2 (HGNC:25774): (tectonic family member 2) This gene encodes a type I membrane protein that belongs to the tectonic family. Studies in mice suggest that this protein may be involved in hedgehog signaling, and essential for ciliogenesis. Mutations in this gene are associated with Meckel syndrome type 8. Alternatively spliced transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Oct 2011]

TCTN2 Gene-Disease associations (from GenCC):

• Joubert syndrome 24

  Inheritance: AR Classification: DEFINITIVE, STRONG, MODERATE Submitted by: ClinGen, G2P, Labcorp Genetics (formerly Invitae), Ambry Genetics
• Joubert syndrome

  Inheritance: AR Classification: SUPPORTIVE Submitted by: Orphanet
• Meckel syndrome

  Inheritance: AR Classification: SUPPORTIVE Submitted by: Orphanet

ACMG classification

Our verdict: Pathogenic. The variant received 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 12-123672116-CTG-C is Pathogenic according to our data. Variant chr12-123672116-CTG-C is described in CliVar as Likely_pathogenic. Clinvar id is 191281.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr12-123672116-CTG-C is described in CliVar as Likely_pathogenic. Clinvar id is 191281.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr12-123672116-CTG-C is described in CliVar as Likely_pathogenic. Clinvar id is 191281.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr12-123672116-CTG-C is described in CliVar as Likely_pathogenic. Clinvar id is 191281.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr12-123672116-CTG-C is described in CliVar as Likely_pathogenic. Clinvar id is 191281.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr12-123672116-CTG-C is described in CliVar as Likely_pathogenic. Clinvar id is 191281.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr12-123672116-CTG-C is described in CliVar as Likely_pathogenic. Clinvar id is 191281.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr12-123672116-CTG-C is described in CliVar as Likely_pathogenic. Clinvar id is 191281.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr12-123672116-CTG-C is described in CliVar as Likely_pathogenic. Clinvar id is 191281.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr12-123672116-CTG-C is described in CliVar as Likely_pathogenic. Clinvar id is 191281.Status of the report is criteria_provided_single_submitter, 1 stars.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TCTN2	NM_024809.5	c.254_255delTG	p.Val85AspfsTer24	frameshift_variant	Exon 3 of 18	ENST00000303372.7	NP_079085.2
TCTN2	NM_001143850.3	c.254_255delTG	p.Val85AspfsTer23	frameshift_variant	Exon 3 of 18		NP_001137322.1
TCTN2	NM_001410989.1	c.254_255delTG	p.Val85AspfsTer24	frameshift_variant	Exon 3 of 17		NP_001397918.1
TCTN2	XM_017019974.2	c.254_255delTG	p.Val85AspfsTer23	frameshift_variant	Exon 3 of 17		XP_016875463.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
TCTN2	ENST00000303372.7	c.254_255delTG	p.Val85AspfsTer24	frameshift_variant	Exon 3 of 18	1	NM_024809.5	ENSP00000304941.5

Frequencies

GnomAD3 genomes Cov.: 32

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

GnomAD4 genome Cov.: 32

ClinVar

Significance: Likely pathogenic

Submissions summary: Pathogenic:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Pathogenic:1

-

Genomic Medicine Center of Excellence, King Faisal Specialist Hospital and Research Centre

Significance: Likely pathogenic

Review Status: criteria provided, single submitter

Collection Method: research

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
PhyloP100		2.1
Mutation Taster		=9/191	disease causing (ClinVar)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.020		Details are displayed if max score is > 0.2

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

Other links and lift over

dbSNP: rs786205622; hg19: chr12-124156663;