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NM_001082538.3(TCTN1):c.736A>T (p.Lys246Ter) AND Joubert syndrome 13

Germline classification:
Pathogenic (1 submission)
Last evaluated:
Nov 3, 2022
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:
RCV002300621.1

Allele description [Variation Report for NM_001082538.3(TCTN1):c.736A>T (p.Lys246Ter)]

NM_001082538.3(TCTN1):c.736A>T (p.Lys246Ter)

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.736A>T (p.Lys246Ter)
HGVS:
  • NC_000012.12:g.110634693A>T
  • NG_030381.1:g.25667A>T
  • NM_001082537.3:c.736A>T
  • NM_001082538.3:c.736A>TMANE SELECT
  • NM_001173975.3:c.568A>T
  • NM_001173976.2:c.556A>T
  • NM_001319680.2:c.736A>T
  • NM_001319681.2:c.202A>T
  • NM_024549.6:c.780+230A>T
  • NP_001076006.1:p.Lys246Ter
  • NP_001076007.1:p.Lys246Ter
  • NP_001167446.1:p.Lys190Ter
  • NP_001167447.1:p.Lys186Ter
  • NP_001306609.1:p.Lys246Ter
  • NP_001306610.1:p.Lys68Ter
  • NC_000012.11:g.111072498A>T
  • NR_135088.2:n.1146A>T
Protein change:
K186*
Links:
dbSNP: rs748215804
NCBI 1000 Genomes Browser:
rs748215804
Molecular consequence:
  • NM_024549.6:c.780+230A>T - intron variant - [Sequence Ontology: SO:0001627]
  • NR_135088.2:n.1146A>T - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NM_001082537.3:c.736A>T - nonsense - [Sequence Ontology: SO:0001587]
  • NM_001082538.3:c.736A>T - nonsense - [Sequence Ontology: SO:0001587]
  • NM_001173975.3:c.568A>T - nonsense - [Sequence Ontology: SO:0001587]
  • NM_001173976.2:c.556A>T - nonsense - [Sequence Ontology: SO:0001587]
  • NM_001319680.2:c.736A>T - nonsense - [Sequence Ontology: SO:0001587]
  • NM_001319681.2:c.202A>T - nonsense - [Sequence Ontology: SO:0001587]
Observations:
1

Condition(s)

Name:
Joubert syndrome 13 (JBTS13)
Identifiers:
MONDO: MONDO:0013608; MedGen: C3280031; Orphanet: 475; OMIM: 614173

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV002588779DASA
criteria provided, single submitter

(ACMG Guidelines, 2015)		Pathogenic
(Nov 3, 2022) 		germlineclinical testing

PubMed (1)
[See all records that cite this PMID]

Help

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineunknown1not providednot providednot providednot providedclinical testing

Citations

PubMed

Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology.

Richards S, Aziz N, Bale S, Bick D, Das S, Gastier-Foster J, Grody WW, Hegde M, Lyon E, Spector E, Voelkerding K, Rehm HL; ACMG Laboratory Quality Assurance Committee..

Genet Med. 2015 May;17(5):405-24. doi: 10.1038/gim.2015.30. Epub 2015 Mar 5.

PubMed [citation]
PMID:
25741868
PMCID:
PMC4544753

Details of each submission

From DASA, SCV002588779.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not provided1not providednot providedclinical testing PubMed (1)

Description

The c.736A>T;p.Lys246* variant creates a premature translational stop signal in the TCTN1 gene. It is expected to result in an absent or disrupted protein product - PVS1. ClinVar contains an entry for this variant (Clinvar ID: 1410963) - PS4_supporting. The variant is present at low allele frequencies population databases (rs748215804 – gnomAD 0.0001225%; ABraOM no frequency - https://abraom.ib.usp.br/) - PM2_supporting. In summary, the currently available evidence indicates that the variant is pathogenic.

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknownnot providednot providednot provided1not providednot providednot provided

Last Updated: Mar 5, 2024