The APTX c.1003C>T (p.His335Tyr) missense variant results in the substitution of histidine at amino acid position 335 with tyrosine. To our knowledge, this variant has not been reported in the peer-reviewed literature. This variant is not found in version 2.1.1 or version 3.1.2 of the Genome Aggregation Database. The c.1003C>T variant lies within the ZNF domain, thought to be important in substrate specificity with His335 as one of four zinc binding residues (PMID: 25637650). Multiple lines of computational evidence suggest the variant may have a deleterious effect on the gene or gene product. Based on the available evidence, the c.1003C>T (p.His335Tyr) variant is classified as a variant of uncertain significance for ataxia with oculomotor apraxia.
ClinVar Genomic variation as it relates to human health
NM_001195248.2(APTX):c.1003C>T (p.His335Tyr)
Germline
Classification
Help
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.
(2)
Help
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.
Uncertain significance
2
criteria provided, multiple submitters, no conflicts
Somatic
No data submitted for somatic clinical impact
Somatic
No data submitted for oncogenicity
Variant Details
- Identifiers
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NM_001195248.2(APTX):c.1003C>T (p.His335Tyr)
Variation ID: 994778 Accession: VCV000994778.4
- Type and length
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single nucleotide variant, 1 bp
- Location
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Cytogenetic: 9p21.1 9: 32973524 (GRCh38) [ NCBI UCSC ] 9: 32973522 (GRCh37) [ NCBI UCSC ]
- Timeline in ClinVar
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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 Jan 26, 2021 Feb 18, 2023 Dec 7, 2022 - HGVS
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... more HGVS ... less HGVSNucleotide Protein Molecular
consequenceNM_001195248.2:c.1003C>T MANE Select Help Transcripts from the Matched Annotation from the NCBI and EMBL-EBI (MANE) collaboration.
NP_001182177.2:p.His335Tyr missense NM_001195249.2:c.1003C>T NP_001182178.1:p.His335Tyr missense NM_001195250.2:c.841C>T NP_001182179.2:p.His281Tyr missense NM_001195251.2:c.*160C>T 3 prime UTR NM_001195252.2:c.787C>T NP_001182181.2:p.His263Tyr missense NM_001195254.2:c.841C>T NP_001182183.1:p.His281Tyr missense NM_001368995.1:c.1003C>T NP_001355924.1:p.His335Tyr missense NM_001368996.1:c.1003C>T NP_001355925.1:p.His335Tyr missense NM_001368997.1:c.1003C>T NP_001355926.1:p.His335Tyr missense NM_001368998.1:c.1003C>T NP_001355927.1:p.His335Tyr missense NM_001368999.1:c.*160C>T 3 prime UTR NM_001369000.1:c.841C>T NP_001355929.1:p.His281Tyr missense NM_001369001.1:c.841C>T NP_001355930.1:p.His281Tyr missense NM_001369002.1:c.739C>T NP_001355931.1:p.His247Tyr missense NM_001369003.1:c.739C>T NP_001355932.1:p.His247Tyr missense NM_001369004.1:c.739C>T NP_001355933.1:p.His247Tyr missense NM_001369005.1:c.739C>T NP_001355934.1:p.His247Tyr missense NM_001369006.1:c.*160C>T 3 prime UTR NM_001370669.1:c.739C>T NP_001357598.1:p.His247Tyr missense NM_001370670.1:c.739C>T NP_001357599.1:p.His247Tyr missense NM_001370673.1:c.739C>T NP_001357602.1:p.His247Tyr missense NM_175069.3:c.*160C>T 3 prime UTR NM_175073.3:c.1003C>T NP_778243.1:p.His335Tyr missense NR_036577.2:n.954C>T non-coding transcript variant NR_160920.1:n.842C>T non-coding transcript variant NR_160921.1:n.973C>T non-coding transcript variant NR_160922.1:n.1204C>T non-coding transcript variant NR_160923.1:n.1008C>T non-coding transcript variant NR_160924.1:n.1013C>T non-coding transcript variant NR_160925.1:n.1209C>T non-coding transcript variant NR_160926.1:n.999C>T non-coding transcript variant NR_160927.1:n.1092C>T non-coding transcript variant NR_160928.1:n.1018C>T non-coding transcript variant NR_160929.1:n.896C>T non-coding transcript variant NR_160930.1:n.949C>T non-coding transcript variant NR_160931.1:n.1188C>T non-coding transcript variant NC_000009.12:g.32973524G>A NC_000009.11:g.32973522G>A NG_012821.2:g.56608C>T - Protein change
- H247Y, H263Y, H281Y, H335Y
- Other names
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- Canonical SPDI
- NC_000009.12:32973523:G:A
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Functional
consequence HelpThe effect of the variant on RNA or protein function, based on experimental evidence from submitters.
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Global minor allele
frequency (GMAF) HelpThe 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.
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Allele frequency
Help
The frequency of the allele represented by this VCV record.
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- Links
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 | ||
|---|---|---|---|---|---|---|
| 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. |
|||
| APTX | - | - |
GRCh38 GRCh37 |
289 | 358 | |
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. |
|---|---|---|---|---|
| Uncertain significance (2) |
criteria provided, multiple submitters, no conflicts
|
Dec 7, 2022 | RCV001288440.5 |
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. |
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|---|---|---|---|---|---|
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Uncertain significance
(Nov 08, 2019)
|
criteria provided, single submitter
Method: clinical testing
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not provided
Affected status: unknown
Allele origin:
unknown
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Athena Diagnostics
Accession: SCV001475536.1
First in ClinVar: Jan 26, 2021 Last updated: Jan 26, 2021 |
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Uncertain significance
(Dec 07, 2022)
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criteria provided, single submitter
Method: clinical testing
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not provided
Affected status: yes
Allele origin:
unknown
|
Illumina Laboratory Services, Illumina
Accession: SCV003802848.1
First in ClinVar: Feb 18, 2023 Last updated: Feb 18, 2023 |
Comment:
The APTX c.1003C>T (p.His335Tyr) missense variant results in the substitution of histidine at amino acid position 335 with tyrosine. To our knowledge, this variant has … (more)
The APTX c.1003C>T (p.His335Tyr) missense variant results in the substitution of histidine at amino acid position 335 with tyrosine. To our knowledge, this variant has not been reported in the peer-reviewed literature. This variant is not found in version 2.1.1 or version 3.1.2 of the Genome Aggregation Database. The c.1003C>T variant lies within the ZNF domain, thought to be important in substrate specificity with His335 as one of four zinc binding residues (PMID: 25637650). Multiple lines of computational evidence suggest the variant may have a deleterious effect on the gene or gene product. Based on the available evidence, the c.1003C>T (p.His335Tyr) variant is classified as a variant of uncertain significance for ataxia with oculomotor apraxia. (less)
|
Comment:
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:
The APTX c.1003C>T (p.His335Tyr) missense variant results in the substitution of histidine at amino acid position 335 with tyrosine. To our knowledge, this variant has not been reported in the peer-reviewed literature. This variant is not found in version 2.1.1 or version 3.1.2 of the Genome Aggregation Database. The c.1003C>T variant lies within the ZNF domain, thought to be important in substrate specificity with His335 as one of four zinc binding residues (PMID: 25637650). Multiple lines of computational evidence suggest the variant may have a deleterious effect on the gene or gene product. Based on the available evidence, the c.1003C>T (p.His335Tyr) variant is classified as a variant of uncertain significance for ataxia with oculomotor apraxia.
Citations for germline classification of this variant
Help| Title | Author | Journal | Year | Link |
|---|---|---|---|---|
| Molecular underpinnings of Aprataxin RNA/DNA deadenylase function and dysfunction in neurological disease. | Schellenberg MJ | Progress in biophysics and molecular biology | 2015 | PMID: 25637650 |
Text-mined citations for rs1828537508 ...
HelpThese 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 May 08, 2024
This date represents the last time this VCV record was updated. The update may be due to an update to one of the included submitted records (SCVs), or due to an update that ClinVar made to the variant such as adding HGVS expressions or a rs number. So this date may be different from the date of the “most recent submission” reported at the top of this page.