NM_001082538.3(TCTN1):c.291C>A (p.Cys97Ter) AND Joubert syndrome and related disorders

Germline classification:: Pathogenic (1 submission)
Last evaluated:: Aug 9, 2024
Review status:: 1 star out of maximum of 4 stars
criteria provided, single submitter

Somatic classification of clinical impact:: None
Review status:: (0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided

Somatic classification of oncogenicity:: None
Review status:: (0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided

Record status:: current
Accession:: RCV004771433.1

Allele description [Variation Report for NM_001082538.3(TCTN1):c.291C>A (p.Cys97Ter)]

NM_001082538.3(TCTN1):c.291C>A (p.Cys97Ter)

Gene:

TCTN1:tectonic family member 1 [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

12q24.11

Genomic location:

Preferred name:

NM_001082538.3(TCTN1):c.291C>A (p.Cys97Ter)

HGVS:

NC_000012.12:g.110619906C>A
NG_030381.1:g.10880C>A
NM_001082537.3:c.291C>A
NM_001082538.3:c.291C>AMANE SELECT
NM_001173975.3:c.123C>A
NM_001173976.2:c.111C>A
NM_001319680.2:c.291C>A
NM_001319681.2:c.-417C>A
NM_001319682.3:c.123C>A
NM_024549.6:c.291C>A
NP_001076006.1:p.Cys97Ter
NP_001076007.1:p.Cys97Ter
NP_001167446.1:p.Cys41Ter
NP_001167447.1:p.Cys37Ter
NP_001306609.1:p.Cys97Ter
NP_001306611.1:p.Cys41Ter
NP_078825.2:p.Cys97Ter
NC_000012.11:g.111057711C>A
NR_135088.2:n.406C>A

Protein change:

C37*

Molecular consequence:

NM_001319681.2:c.-417C>A - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NR_135088.2:n.406C>A - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NM_001082537.3:c.291C>A - nonsense - [Sequence Ontology: SO:0001587]
NM_001082538.3:c.291C>A - nonsense - [Sequence Ontology: SO:0001587]
NM_001173975.3:c.123C>A - nonsense - [Sequence Ontology: SO:0001587]
NM_001173976.2:c.111C>A - nonsense - [Sequence Ontology: SO:0001587]
NM_001319680.2:c.291C>A - nonsense - [Sequence Ontology: SO:0001587]
NM_001319682.3:c.123C>A - nonsense - [Sequence Ontology: SO:0001587]
NM_024549.6:c.291C>A - nonsense - [Sequence Ontology: SO:0001587]

Condition(s)

Name:: Joubert syndrome and related disorders
Identifiers:: MONDO: MONDO:0015369; MedGen: C5679612

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV005380723	Women's Health and Genetics/Laboratory Corporation of America, LabCorp	criteria provided, single submitter (LabCorp Variant Classification Summary - May 2015)	Pathogenic (Aug 9, 2024)	germline	clinical testing	Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV005380723

Women's Health and Genetics/Laboratory Corporation of America, LabCorp

criteria provided, single submitter

(LabCorp Variant Classification Summary - May 2015)

Pathogenic
(Aug 9, 2024)

germline

clinical testing

Citation Link

Help

Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	germline	unknown	not provided	not provided	not provided	not provided	not provided	clinical testing

Details of each submission

From Women's Health and Genetics/Laboratory Corporation of America, LabCorp, SCV005380723.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	not provided

Description

Variant summary: TCTN1 c.291C>A (p.Cys97X) results in a premature termination codon, predicted to cause absence of the protein due to nonsense mediated decay, which is a commonly known mechanism for disease. The variant allele was found at a frequency of 4e-06 in 249586 control chromosomes. To our knowledge, no occurrence of c.291C>A in individuals affected with Joubert Syndrome And Related Disorders and no experimental evidence demonstrating its impact on protein function have been reported. No submitters have cited clinical-significance assessments for this variant to ClinVar. Based on the evidence outlined above, the variant was classified as pathogenic.

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	unknown	not provided	not provided	not provided		not provided	not provided	not provided	not provided

Last Updated: Apr 7, 2025

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