VCV000383137.21 - ClinVar

NM_021830.5(TWNK):c.1609T>C (p.Tyr537His)

Germline

Classification

The aggregate germline classification for this variant, typically for a monogenic or Mendelian disorder as in the ACMG/AMP guidelines, or for response to a drug. This value is calculated by NCBI based on data from submitters. Read our rules for calculating the aggregate classification.

(10)

Stars represent the aggregate review status, or the level of review supporting the aggregate germline classification for this VCV record. This value is calculated by NCBI based on data from submitters. Read our rules for calculating the review status. The number of submissions which contribute to this review status is shown in parentheses.

Conflicting classifications of pathogenicity
Uncertain significance(8); Benign(2)

criteria provided, conflicting classifications

Somatic

No data submitted for somatic clinical impact

Somatic

No data submitted for oncogenicity

Variant Details

Identifiers

NM_021830.5(TWNK):c.1609T>C (p.Tyr537His)

Variation ID: 383137 Accession: VCV000383137.21

Type and length

single nucleotide variant, 1 bp

Location

Cytogenetic: 10q24.31 10: 100990885 (GRCh38) [ NCBI UCSC ] 10: 102750642 (GRCh37) [ NCBI UCSC ]

Timeline in ClinVar

	First in ClinVar Help The date this variant first appeared in ClinVar with each type of classification.	Last submission Help The date of the most recent submission for each type of classification for this variant.	Last evaluated Help The most recent date that a submitter evaluated this variant for each type of classification.
Germline	Dec 19, 2017	Jul 23, 2024	May 1, 2024

HGVS

Nucleotide	Protein	Molecular consequence
NM_021830.5:c.1609T>C MANE Select Help Transcripts from the Matched Annotation from the NCBI and EMBL-EBI (MANE) collaboration.	NP_068602.2:p.Tyr537His	missense
NM_001163812.2:c.1609T>C	NP_001157284.1:p.Tyr537His	missense
NM_001163813.2:c.247T>C	NP_001157285.1:p.Tyr83His	missense
NM_001163814.2:c.247T>C	NP_001157286.1:p.Tyr83His	missense
NM_001368275.1:c.247T>C	NP_001355204.1:p.Tyr83His	missense
NR_160738.1:n.2397T>C		non-coding transcript variant
NR_160739.1:n.557T>C		non-coding transcript variant
NR_160740.1:n.2215T>C		non-coding transcript variant
NR_160741.1:n.2215T>C		non-coding transcript variant
NR_160742.1:n.2335T>C		non-coding transcript variant
NC_000010.11:g.100990885T>C
NC_000010.10:g.102750642T>C
NG_011646.1:g.1631A>G
NG_012624.1:g.8350T>C

... more HGVS ... less HGVS

Protein change

Y537H, Y83H

Other names

Canonical SPDI

NC_000010.11:100990884:T:C

Functional consequence Help The effect of the variant on RNA or protein function, based on experimental evidence from submitters.

Global minor allele frequency (GMAF) Help The global minor allele frequency calculated by the 1000 Genomes Project. The minor allele at this location is indicated in parentheses and may be different from the allele represented by this VCV record.

Allele frequency Help The frequency of the allele represented by this VCV record.

Exome Aggregation Consortium (ExAC) 0.00013

The Genome Aggregation Database (gnomAD), exomes 0.00015

The Genome Aggregation Database (gnomAD) 0.00021

Trans-Omics for Precision Medicine (TOPMed) 0.00024

NHLBI Exome Sequencing Project (ESP) Exome Variant Server 0.00031

Links

ClinGen: CA5653294 dbSNP: rs144001072 VarSome

Genes

Gene	OMIM	ClinGen Gene Dosage Sensitivity Curation		Variation Viewer Help Links to Variation Viewer, a genome browser to view variation data from NCBI databases.	Related variants
Gene	OMIM	HI score Help The haploinsufficiency score for the gene, curated by ClinGen’s Dosage Sensitivity Curation task team.	TS score Help The triplosensitivity score for the gene, curated by ClinGen’s Dosage Sensitivity Curation task team.		Within gene Help The number of variants in ClinVar that are contained within this gene, with a link to view the list of variants.	All Help The number of variants in ClinVar for this gene, including smaller variants within the gene and larger CNVs that overlap or fully contain the gene.
TWNK		-	-	GRCh38 GRCh37	536	553

Conditions - Germline

Condition Help The condition for this variant-condition (RCV) record in ClinVar.	Classification Help The aggregate germline classification for this variant-condition (RCV) record in ClinVar. The number of submissions that contribute to this aggregate classification is shown in parentheses. (# of submissions)	Review status Help The aggregate review status for this variant-condition (RCV) record in ClinVar. This value is calculated by NCBI based on data from submitters. Read our rules for calculating the review status.	Last evaluated Help The most recent date that a submitter evaluated this variant for the condition.	Variation/condition record Help The RCV accession number, with most recent version number, for the variant-condition record, with a link to the RCV web page.
not provided	Uncertain significance (3)	criteria provided, multiple submitters, no conflicts	May 1, 2024	RCV000726623.13
Sensory ataxic neuropathy, dysarthria, and ophthalmoparesis	Benign (1)	criteria provided, single submitter	Apr 28, 2017	RCV001105999.4
Progressive external ophthalmoplegia with mitochondrial DNA deletions, autosomal dominant 3	Benign (1)	criteria provided, single submitter	Apr 28, 2017	RCV001105997.4
Autosomal recessive cerebellar ataxia	Uncertain significance (1)	criteria provided, single submitter	Apr 28, 2017	RCV001105998.4
Infantile onset spinocerebellar ataxia	Uncertain significance (1)	criteria provided, single submitter	Apr 28, 2017	RCV001106000.4
Hereditary spastic paraplegia	Uncertain significance (1)	criteria provided, single submitter	Sep 30, 2020	RCV001848766.3
not specified	Uncertain significance (1)	criteria provided, single submitter	Feb 7, 2024	RCV003993959.1
TWNK-related disorder	Uncertain significance (1)	criteria provided, single submitter	Sep 3, 2023	RCV004533016.1

Submissions - Germline

Classification Help The submitted germline classification for each SCV record. (Last evaluated)	Review status Help Stars represent the review status, or the level of review supporting the submitted (SCV) record. This value is calculated by NCBI based on data from the submitter. Read our rules for calculating the review status. This column also includes a link to the submitter’s assertion criteria if provided, and the collection method. (Assertion criteria)	Condition Help The condition for the classification, provided by the submitter for this submitted (SCV) record. This column also includes the affected status and allele origin of individuals observed with this variant.	Submitter Help The submitting organization for this submitted (SCV) record. This column also includes the SCV accession and version number, the date this SCV first appeared in ClinVar, and the date that this SCV was last updated in ClinVar.	More information Help This column includes more information supporting the classification, including citations, the comment on classification, and detailed evidence provided as observations of the variant by the submitter.
Uncertain significance (Oct 12, 2016)	criteria provided, single submitter (EGL Classification Definitions 2015) Method: clinical testing	not provided Affected status: unknown Allele origin: germline	Eurofins Ntd Llc (ga) Accession: SCV000701817.2 First in ClinVar: Dec 19, 2017 Last updated: Dec 15, 2018	Other databases http://www.egl-eurofins.com/emvc… http://www.egl-eurofins.com/emvclass/emvclass.php?approved_symbol=TWNK Number of individuals with the variant: 1 Sex: mixed
Uncertain significance (Apr 28, 2017)	criteria provided, single submitter (ICSL Variant Classification Criteria 13 December 2019) Method: clinical testing	Autosomal recessive cerebellar ataxia Affected status: unknown Allele origin: germline	Illumina Laboratory Services, Illumina Accession: SCV001263022.1 First in ClinVar: May 31, 2020 Last updated: May 31, 2020	Comment: This variant was observed as part of a predisposition screen in an ostensibly healthy population. A literature search was performed for the gene, cDNA change, … (more) This variant was observed as part of a predisposition screen in an ostensibly healthy population. A literature search was performed for the gene, cDNA change, and amino acid change (where applicable). No publications were found based on this search. Allele frequency data from public databases did not allow this variant to be ruled in or out of causing disease. Therefore, this variant is classified as a variant of unknown significance. (less)
Benign (Apr 28, 2017)	criteria provided, single submitter (ICSL Variant Classification Criteria 13 December 2019) Method: clinical testing	Progressive external ophthalmoplegia with mitochondrial DNA deletions, autosomal dominant 3 Affected status: unknown Allele origin: germline	Illumina Laboratory Services, Illumina Accession: SCV001263021.1 First in ClinVar: May 31, 2020 Last updated: May 31, 2020	Publications: PubMed (1) PubMed: 21689831 Comment: This variant was observed as part of a predisposition screen in an ostensibly healthy population. A literature search was performed for the gene, cDNA change, … (more) This variant was observed as part of a predisposition screen in an ostensibly healthy population. A literature search was performed for the gene, cDNA change, and amino acid change (where applicable). Publications were found based on this search. The evidence from the literature, in combination with allele frequency data from public databases where available, was sufficient to rule this variant out of causing disease. Therefore, this variant is classified as benign. (less)
Benign (Apr 28, 2017)	criteria provided, single submitter (ICSL Variant Classification Criteria 13 December 2019) Method: clinical testing	Sensory ataxic neuropathy-dysarthria-ophthalmoparesis syndrome Affected status: unknown Allele origin: germline	Illumina Laboratory Services, Illumina Accession: SCV001263023.1 First in ClinVar: May 31, 2020 Last updated: May 31, 2020	Comment: This variant was observed as part of a predisposition screen in an ostensibly healthy population. A literature search was performed for the gene, cDNA change, … (more) This variant was observed as part of a predisposition screen in an ostensibly healthy population. A literature search was performed for the gene, cDNA change, and amino acid change (where applicable). No publications were found based on this search. Allele frequency data from public databases was too high to be consistent with this variant causing disease. Therefore, this variant is classified as benign. (less)
Uncertain significance (Apr 28, 2017)	criteria provided, single submitter (ICSL Variant Classification Criteria 13 December 2019) Method: clinical testing	Infantile onset spinocerebellar ataxia Affected status: unknown Allele origin: germline	Illumina Laboratory Services, Illumina Accession: SCV001263024.1 First in ClinVar: May 31, 2020 Last updated: May 31, 2020	Comment: This variant was observed as part of a predisposition screen in an ostensibly healthy population. A literature search was performed for the gene, cDNA change, … (more) This variant was observed as part of a predisposition screen in an ostensibly healthy population. A literature search was performed for the gene, cDNA change, and amino acid change (where applicable). No publications were found based on this search. Allele frequency data from public databases did not allow this variant to be ruled in or out of causing disease. Therefore, this variant is classified as a variant of unknown significance. (less)
Uncertain significance (May 01, 2024)	criteria provided, single submitter (GeneDx Variant Classification Process June 2021) Method: clinical testing	Not Provided Affected status: yes Allele origin: germline	GeneDx Accession: SCV000523428.6 First in ClinVar: Mar 08, 2017 Last updated: Jul 23, 2024	Comment: In silico analysis indicates that this missense variant does not alter protein structure/function; This variant is associated with the following publications: (PMID: 26615986, 35792653, 21689831)
Uncertain significance (Sep 30, 2020)	criteria provided, single submitter (ACMG Guidelines, 2015) Method: clinical testing	Hereditary spastic paraplegia Affected status: yes Allele origin: germline	Genome Diagnostics Laboratory, The Hospital for Sick Children Accession: SCV002106278.1 First in ClinVar: Mar 19, 2022 Last updated: Mar 19, 2022
Uncertain significance (Sep 03, 2023)	criteria provided, single submitter (ACMG Guidelines, 2015) Method: clinical testing	TWNK-related condition Affected status: unknown Allele origin: germline	PreventionGenetics, part of Exact Sciences Accession: SCV004113941.1 First in ClinVar: Nov 20, 2023 Last updated: Nov 20, 2023	Comment: The TWNK c.1609T>C variant is predicted to result in the amino acid substitution p.Tyr537His. This variant was reported in the heterozygous state in individuals with … (more) The TWNK c.1609T>C variant is predicted to result in the amino acid substitution p.Tyr537His. This variant was reported in the heterozygous state in individuals with chronic external ophthalmoplegia or Parkinson's disease; however, pathogenicity was not established (Ronchi et al. 2011. PubMed ID: 21689831; Percetti et al. 2022. PubMed ID: 35792653). This variant is reported in 0.029% of alleles in individuals of European (Non-Finnish) descent in gnomAD (http://gnomad.broadinstitute.org/variant/10-102750642-T-C), which may be too frequent to be a primary cause of autosomal dominant disease. Although we suspect TWNK c.1609T>C (p.Tyr537His) may be benign, the clinical significance of this variant is uncertain due to the absence of conclusive functional and genetic evidence. (less)
Uncertain significance (Jan 23, 2024)	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015)) Method: clinical testing	not provided Affected status: unknown Allele origin: germline	Labcorp Genetics (formerly Invitae), Labcorp Accession: SCV002295990.3 First in ClinVar: Mar 28, 2022 Last updated: Feb 28, 2024	Publications: PubMed (1) PubMed: 21689831 Comment: This sequence change replaces tyrosine, which is neutral and polar, with histidine, which is basic and polar, at codon 537 of the TWNK protein (p.Tyr537His). … (more) This sequence change replaces tyrosine, which is neutral and polar, with histidine, which is basic and polar, at codon 537 of the TWNK protein (p.Tyr537His). This variant is present in population databases (rs144001072, gnomAD 0.03%). This missense change has been observed in individual(s) with clinical features of TWNK-related conditions (PMID: 21689831). ClinVar contains an entry for this variant (Variation ID: 383137). Advanced modeling of protein sequence and biophysical properties (such as structural, functional, and spatial information, amino acid conservation, physicochemical variation, residue mobility, and thermodynamic stability) performed at Invitae indicates that this missense variant is not expected to disrupt TWNK protein function with a negative predictive value of 80%. 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. (less)
Uncertain significance (Feb 07, 2024)	criteria provided, single submitter (LabCorp Variant Classification Summary - May 2015) Method: clinical testing	not specified Affected status: unknown Allele origin: germline	Women's Health and Genetics/Laboratory Corporation of America, LabCorp Accession: SCV004813212.1 First in ClinVar: Apr 15, 2024 Last updated: Apr 15, 2024	Publications: PubMed (1) PubMed: 21689831 Comment: Variant summary: TWNK c.1609T>C (p.Tyr537His) results in a conservative amino acid change located in the DNA helicase, DnaB-like, C-terminal (IPR007694) of the encoded protein sequence. … (more) Variant summary: TWNK c.1609T>C (p.Tyr537His) results in a conservative amino acid change located in the DNA helicase, DnaB-like, C-terminal (IPR007694) of the encoded protein sequence. Four of five in-silico tools predict a benign effect of the variant on protein function. The variant allele was found at a frequency of 0.00038 in 1614126 control chromosomes in the gnomAD database (v4.0.0), including 1 homozygotes c.1609T>C has been reported in the literature in individuals affected with Opthalmoplegia (Ronchi_2011). This report does not provide unequivocal conclusions about association of the variant with Infantile Onset Spinocerebellar Ataxia. To our knowledge, no experimental evidence demonstrating an impact on protein function has been reported. The following publication have been ascertained in the context of this evaluation (PMID: 21689831). ClinVar contains an entry for this variant (Variation ID: 383137). Based on the evidence outlined above, the variant was classified as uncertain significance. (less)

Comment:

This variant was observed as part of a predisposition screen in an ostensibly healthy population. A literature search was performed for the gene, cDNA change, and amino acid change (where applicable). No publications were found based on this search. Allele frequency data from public databases did not allow this variant to be ruled in or out of causing disease. Therefore, this variant is classified as a variant of unknown significance.

Comment:

This variant was observed as part of a predisposition screen in an ostensibly healthy population. A literature search was performed for the gene, cDNA change, and amino acid change (where applicable). Publications were found based on this search. The evidence from the literature, in combination with allele frequency data from public databases where available, was sufficient to rule this variant out of causing disease. Therefore, this variant is classified as benign.

Comment:

This variant was observed as part of a predisposition screen in an ostensibly healthy population. A literature search was performed for the gene, cDNA change, and amino acid change (where applicable). No publications were found based on this search. Allele frequency data from public databases was too high to be consistent with this variant causing disease. Therefore, this variant is classified as benign.

Comment:

The TWNK c.1609T>C variant is predicted to result in the amino acid substitution p.Tyr537His. This variant was reported in the heterozygous state in individuals with chronic external ophthalmoplegia or Parkinson's disease; however, pathogenicity was not established (Ronchi et al. 2011. PubMed ID: 21689831; Percetti et al. 2022. PubMed ID: 35792653). This variant is reported in 0.029% of alleles in individuals of European (Non-Finnish) descent in gnomAD (http://gnomad.broadinstitute.org/variant/10-102750642-T-C), which may be too frequent to be a primary cause of autosomal dominant disease. Although we suspect TWNK c.1609T>C (p.Tyr537His) may be benign, the clinical significance of this variant is uncertain due to the absence of conclusive functional and genetic evidence.

Comment:

This sequence change replaces tyrosine, which is neutral and polar, with histidine, which is basic and polar, at codon 537 of the TWNK protein (p.Tyr537His). This variant is present in population databases (rs144001072, gnomAD 0.03%). This missense change has been observed in individual(s) with clinical features of TWNK-related conditions (PMID: 21689831). ClinVar contains an entry for this variant (Variation ID: 383137). Advanced modeling of protein sequence and biophysical properties (such as structural, functional, and spatial information, amino acid conservation, physicochemical variation, residue mobility, and thermodynamic stability) performed at Invitae indicates that this missense variant is not expected to disrupt TWNK protein function with a negative predictive value of 80%. 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.

Comment:

Variant summary: TWNK c.1609T>C (p.Tyr537His) results in a conservative amino acid change located in the DNA helicase, DnaB-like, C-terminal (IPR007694) of the encoded protein sequence. Four of five in-silico tools predict a benign effect of the variant on protein function. The variant allele was found at a frequency of 0.00038 in 1614126 control chromosomes in the gnomAD database (v4.0.0), including 1 homozygotes c.1609T>C has been reported in the literature in individuals affected with Opthalmoplegia (Ronchi_2011). This report does not provide unequivocal conclusions about association of the variant with Infantile Onset Spinocerebellar Ataxia. To our knowledge, no experimental evidence demonstrating an impact on protein function has been reported. The following publication have been ascertained in the context of this evaluation (PMID: 21689831). ClinVar contains an entry for this variant (Variation ID: 383137). Based on the evidence outlined above, the variant was classified as uncertain significance.

Germline Functional Evidence

There is no functional evidence in ClinVar for this variation. If you have generated functional data for this variation, please consider submitting that data to ClinVar.

Comment:

This variant was observed as part of a predisposition screen in an ostensibly healthy population. A literature search was performed for the gene, cDNA change, and amino acid change (where applicable). Publications were found based on this search. The evidence from the literature, in combination with allele frequency data from public databases where available, was sufficient to rule this variant out of causing disease. Therefore, this variant is classified as benign.

Comment:

This variant was observed as part of a predisposition screen in an ostensibly healthy population. A literature search was performed for the gene, cDNA change, and amino acid change (where applicable). No publications were found based on this search. Allele frequency data from public databases was too high to be consistent with this variant causing disease. Therefore, this variant is classified as benign.

Comment:

Citations for germline classification of this variant

Title	Author	Journal	Year	Link
Two novel mutations in PEO1 (twinkle) gene associated with chronic external ophthalmoplegia.	Ronchi D	Journal of the neurological sciences	2011	PMID: 21689831
http://www.egl-eurofins.com/emvclass/emvclass.php?approved_symbol=TWNK	-	-	-	-

Text-mined citations for rs144001072 ...

These citations are identified by LitVar using the rs number, so they may include citations for more than one variant at this location. Please review the LitVar results carefully for your variant of interest.

Record last updated Nov 25, 2024

ClinVar Genomic variation as it relates to human health

NM_021830.5(TWNK):c.1609T>C (p.Tyr537His)

Variant Details

Genes

Conditions - Germline

Submissions - Germline

Germline Functional Evidence

Citations for germline classification of this variant

Text-mined citations for rs144001072 ...