NM_173500.4(TTBK2):c.3722A>C (p.Lys1241Thr) AND not provided

Germline classification:: Conflicting interpretations of pathogenicity (3 submissions)
Last evaluated:: Feb 24, 2023
Review status:: criteria provided, conflicting classifications

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:: RCV000488259.10

Allele description [Variation Report for NM_173500.4(TTBK2):c.3722A>C (p.Lys1241Thr)]

NM_173500.4(TTBK2):c.3722A>C (p.Lys1241Thr)

Gene:

TTBK2:tau tubulin kinase 2 [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

15q15.2

Genomic location:

Preferred name:

NM_173500.4(TTBK2):c.3722A>C (p.Lys1241Thr)

HGVS:

NC_000015.10:g.42745808T>G
NG_012664.1:g.180002A>C
NM_173500.4:c.3722A>CMANE SELECT
NP_775771.3:p.Lys1241Thr
NC_000015.9:g.43038006T>G
NM_173500.3:c.3722A>C

Protein change:

K1241T

Links:

dbSNP: rs36104367

NCBI 1000 Genomes Browser:

rs36104367

Molecular consequence:

NM_173500.4:c.3722A>C - missense variant - [Sequence Ontology: SO:0001583]

Observations:

Condition(s)

Synonyms:: none provided
Identifiers:: MedGen: C3661900

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000575004	CeGaT Center for Human Genetics Tuebingen	criteria provided, single submitter (Praxis fuer Humangenetik Tuebingen - Variant Classification Criteria)	Uncertain significance (Sep 30, 2016)	germline	clinical testing	Citation Link,
SCV001477039	Athena Diagnostics	criteria provided, single submitter (Athena Diagnostics Criteria)	Likely benign (Jan 2, 2020)	unknown	clinical testing	PubMed (1) [See all records that cite this PMID]
SCV003274982	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (Feb 24, 2023)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000575004

CeGaT Center for Human Genetics Tuebingen

criteria provided, single submitter

(Praxis fuer Humangenetik Tuebingen - Variant Classification Criteria)

Uncertain significance
(Sep 30, 2016)

germline

clinical testing

Citation Link,

SCV001477039

Athena Diagnostics

criteria provided, single submitter

(Athena Diagnostics Criteria)

Likely benign
(Jan 2, 2020)

unknown

clinical testing

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

SCV003274982

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(Feb 24, 2023)

germline

clinical testing

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

Help

Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	germline	yes	3	not provided	not provided	not provided	not provided	clinical testing
not provided	germline	unknown	not provided	not provided	not provided	not provided	not provided	clinical testing
not provided	unknown	unknown	not provided	not provided	not provided	not provided	not provided	clinical testing

Citations

PubMed

A Standardized DNA Variant Scoring System for Pathogenicity Assessments in Mendelian Disorders.

Karbassi I, Maston GA, Love A, DiVincenzo C, Braastad CD, Elzinga CD, Bright AR, Previte D, Zhang K, Rowland CM, McCarthy M, Lapierre JL, Dubois F, Medeiros KA, Batish SD, Jones J, Liaquat K, Hoffman CA, Jaremko M, Wang Z, Sun W, Buller-Burckle A, et al.

Hum Mutat. 2016 Jan;37(1):127-34. doi: 10.1002/humu.22918. Epub 2015 Oct 29.

PubMed [citation]

PMID:: 26467025
PMCID:: PMC4737317

Sherloc: a comprehensive refinement of the ACMG-AMP variant classification criteria.

Nykamp K, Anderson M, Powers M, Garcia J, Herrera B, Ho YY, Kobayashi Y, Patil N, Thusberg J, Westbrook M; Invitae Clinical Genomics Group., Topper S.

Genet Med. 2017 Oct;19(10):1105-1117. doi: 10.1038/gim.2017.37. Epub 2017 May 11. Erratum in: Genet Med. 2020 Jan;22(1):240. doi: 10.1038/s41436-019-0624-9.

PubMed [citation]

PMID:: 28492532
PMCID:: PMC5632818

Details of each submission

From CeGaT Center for Human Genetics Tuebingen, SCV000575004.6

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	3	not provided	not provided	clinical testing	not provided

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	yes	not provided	not provided	not provided		3	not provided	not provided	not provided

From Athena Diagnostics, SCV001477039.1

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

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

From Labcorp Genetics (formerly Invitae), Labcorp, SCV003274982.2

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

Description

This variant is present in population databases (rs36104367, gnomAD 0.02%). ClinVar contains an entry for this variant (Variation ID: 425066). This variant has not been reported in the literature in individuals affected with TTBK2-related conditions. This sequence change replaces lysine, which is basic and polar, with threonine, which is neutral and polar, at codon 1241 of the TTBK2 protein (p.Lys1241Thr). An algorithm developed to predict the effect of missense changes on protein structure and function (PolyPhen-2) suggests that this variant is likely to be disruptive. In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance.

#	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: Sep 29, 2024

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