The c.1658C>A (p.T553N) alteration is located in exon 11 (coding exon 10) of the USP19 gene. This alteration results from a C to A substitution at nucleotide position 1658, causing the threonine (T) at amino acid position 553 to be replaced by an asparagine (N). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear.
ClinVar Genomic variation as it relates to human health
NM_001199161.2(USP19):c.1664C>A (p.Thr555Asn)
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.
(1)
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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
1
criteria provided, single submitter
Somatic
No data submitted for somatic clinical impact
Somatic
No data submitted for oncogenicity
Variant Details
- Identifiers
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NM_001199161.2(USP19):c.1664C>A (p.Thr555Asn)
Variation ID: 2371430 Accession: VCV002371430.3
- Type and length
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single nucleotide variant, 1 bp
- Location
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Cytogenetic: 3p21.31 3: 49115752 (GRCh38) [ NCBI UCSC ] 3: 49153185 (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 Feb 8, 2023 Jan 13, 2025 Jul 21, 2024 - HGVS
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... more HGVS ... less HGVSNucleotide Protein Molecular
consequenceNM_001199161.2:c.1664C>A MANE Select Help Transcripts from the Matched Annotation from the NCBI and EMBL-EBI (MANE) collaboration.
NP_001186090.1:p.Thr555Asn missense NM_001199160.2:c.1658C>A NP_001186089.1:p.Thr553Asn missense NM_001199162.2:c.1628C>A NP_001186091.1:p.Thr543Asn missense NM_001351098.2:c.1625C>A NP_001338027.1:p.Thr542Asn missense NM_001351099.2:c.1655C>A NP_001338028.1:p.Thr552Asn missense NM_001351100.2:c.1661C>A NP_001338029.1:p.Thr554Asn missense NM_001351101.2:c.1664C>A NP_001338030.1:p.Thr555Asn missense NM_001351102.2:c.1316C>A NP_001338031.1:p.Thr439Asn missense NM_001351103.2:c.1361C>A NP_001338032.1:p.Thr454Asn missense NM_001351104.2:c.1367C>A NP_001338033.1:p.Thr456Asn missense NM_001351105.2:c.1508C>A NP_001338034.1:p.Thr503Asn missense NM_001351106.2:c.1361C>A NP_001338035.1:p.Thr454Asn missense NM_001351107.2:c.1619C>A NP_001338036.1:p.Thr540Asn missense NM_001351108.2:c.1322C>A NP_001338037.1:p.Thr441Asn missense NM_001389594.1:c.1664C>A NP_001376523.1:p.Thr555Asn missense NM_001389595.1:c.1664C>A NP_001376524.1:p.Thr555Asn missense NM_001389596.1:c.1670C>A NP_001376525.1:p.Thr557Asn missense NM_001389597.1:c.1367C>A NP_001376526.1:p.Thr456Asn missense NM_001389598.1:c.1658C>A NP_001376527.1:p.Thr553Asn missense NM_001389599.1:c.1616C>A NP_001376528.1:p.Thr539Asn missense NM_001389600.1:c.1613C>A NP_001376529.1:p.Thr538Asn missense NM_001389601.1:c.1613C>A NP_001376530.1:p.Thr538Asn missense NM_001389602.1:c.1655C>A NP_001376531.1:p.Thr552Asn missense NM_001389603.1:c.1619C>A NP_001376532.1:p.Thr540Asn missense NM_001389604.1:c.1661C>A NP_001376533.1:p.Thr554Asn missense NM_001389605.1:c.1508C>A NP_001376534.1:p.Thr503Asn missense NM_001389606.1:c.1361C>A NP_001376535.1:p.Thr454Asn missense NM_001389607.1:c.1316C>A NP_001376536.1:p.Thr439Asn missense NM_001389608.1:c.1355C>A NP_001376537.1:p.Thr452Asn missense NM_001400288.1:c.1664C>A NP_001387217.1:p.Thr555Asn missense NM_001400290.1:c.1667C>A NP_001387219.1:p.Thr556Asn missense NM_001400292.1:c.1664C>A NP_001387221.1:p.Thr555Asn missense NM_001400293.1:c.1658C>A NP_001387222.1:p.Thr553Asn missense NM_001400294.1:c.1658C>A NP_001387223.1:p.Thr553Asn missense NM_001400295.1:c.1622C>A NP_001387224.1:p.Thr541Asn missense NM_001400296.1:c.1619C>A NP_001387225.1:p.Thr540Asn missense NM_001400297.1:c.1619C>A NP_001387226.1:p.Thr540Asn missense NM_001400298.1:c.1610C>A NP_001387227.1:p.Thr537Asn missense NM_001400299.1:c.1589C>A NP_001387228.1:p.Thr530Asn missense NM_006677.3:c.1355C>A NP_006668.1:p.Thr452Asn missense NC_000003.12:g.49115752G>T NC_000003.11:g.49153185G>T NG_054716.1:g.10187C>A - Protein change
- T452N, T537N, T540N, T456N, T503N, T539N, T552N, T439N, T454N, T530N, T538N, T543N, T553N, T556N, T441N, T541N, T542N, T554N, T555N, T557N
- Other names
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- Canonical SPDI
- NC_000003.12:49115751:G:T
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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 | ||
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| 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. |
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| USP19 | - | - |
GRCh38 GRCh37 |
129 | 143 | |
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 (1) |
criteria provided, single submitter
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Jul 21, 2024 | RCV004212269.2 |
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
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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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Uncertain significance
(Jul 21, 2024)
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criteria provided, single submitter
Method: clinical testing
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not specified
Affected status: unknown
Allele origin:
germline
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Ambry Genetics
Accession: SCV003709284.3
First in ClinVar: Feb 07, 2023 Last updated: Jan 13, 2025 |
Comment:
The c.1658C>A (p.T553N) alteration is located in exon 11 (coding exon 10) of the USP19 gene. This alteration results from a C to A substitution … (more)
The c.1658C>A (p.T553N) alteration is located in exon 11 (coding exon 10) of the USP19 gene. This alteration results from a C to A substitution at nucleotide position 1658, causing the threonine (T) at amino acid position 553 to be replaced by an asparagine (N). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. (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 c.1658C>A (p.T553N) alteration is located in exon 11 (coding exon 10) of the USP19 gene. This alteration results from a C to A substitution at nucleotide position 1658, causing the threonine (T) at amino acid position 553 to be replaced by an asparagine (N). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear.
Citations for germline classification of this variant
Help| There are no citations for germline classification of this variant in ClinVar. If you know of citations for this variation, please consider submitting that information to ClinVar. |
Text-mined citations for this variant ...
HelpRecord last updated Jan 13, 2025
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.