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NM_001082538.3(TCTN1):c.689T>C (p.Leu230Pro) AND Joubert syndrome 13

Germline classification:
Uncertain significance (1 submission)
Last evaluated:
Jun 15, 2018
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:
RCV000785896.2

Allele description [Variation Report for NM_001082538.3(TCTN1):c.689T>C (p.Leu230Pro)]

NM_001082538.3(TCTN1):c.689T>C (p.Leu230Pro)

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.689T>C (p.Leu230Pro)
HGVS:
  • NC_000012.12:g.110632536T>C
  • NG_030381.1:g.23510T>C
  • NM_001082537.3:c.689T>C
  • NM_001082538.3:c.689T>CMANE SELECT
  • NM_001173975.3:c.521T>C
  • NM_001173976.2:c.509T>C
  • NM_001319680.2:c.689T>C
  • NM_001319681.2:c.155T>C
  • NM_024549.6:c.689T>C
  • NP_001076006.1:p.Leu230Pro
  • NP_001076007.1:p.Leu230Pro
  • NP_001167446.1:p.Leu174Pro
  • NP_001167447.1:p.Leu170Pro
  • NP_001306609.1:p.Leu230Pro
  • NP_001306610.1:p.Leu52Pro
  • NP_078825.2:p.Leu230Pro
  • NC_000012.11:g.111070341T>C
  • NR_135088.2:n.1099T>C
Protein change:
L170P
Links:
dbSNP: rs1225241777
NCBI 1000 Genomes Browser:
rs1225241777
Molecular consequence:
  • NM_001082537.3:c.689T>C - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001082538.3:c.689T>C - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001173975.3:c.521T>C - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001173976.2:c.509T>C - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001319680.2:c.689T>C - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001319681.2:c.155T>C - missense variant - [Sequence Ontology: SO:0001583]
  • NM_024549.6:c.689T>C - missense variant - [Sequence Ontology: SO:0001583]
  • NR_135088.2:n.1099T>C - non-coding transcript variant - [Sequence Ontology: SO:0001619]

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
SCV000924472Broad Center for Mendelian Genomics, Broad Institute of MIT and Harvard
criteria provided, single submitter

(ACMG Guidelines, 2015)		Uncertain significance
(Jun 15, 2018) 		germlineresearch

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

Help

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineyesnot providednot providednot providednot providednot providedresearch

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 Broad Center for Mendelian Genomics, Broad Institute of MIT and Harvard, SCV000924472.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedresearch PubMed (1)

Description

The heterozygous p.Leu230Pro variant was identified by our study in the compound heterozygous state, with another VUS, in one individual with Joubert syndrome. This variant has been identified in <0.01% (1/111676) of European (Non-Finnish) chromosomes by the Genome Aggregation Database (gnomAD, http://gnomad.broadinstitute.org;). Although this variant has been seen in the general population, its frequency is low enough to be consistent with a recessive carrier frequency. The Leucine (Leu) at position 230 is not highly conserved in mammals and evolutionarily distant species, raising the possibility that a change at this position may be tolerated. Computational prediction tools do not provide strong support for or against an impact to the protein. In summary, the clinical significance of this variant is uncertain.

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineyesnot providednot providednot providednot providednot providednot providednot provided

Last Updated: Mar 30, 2024