This sequence change replaces histidine, which is basic and polar, with tyrosine, which is neutral and polar, at codon 7 of the SUN1 protein (p.His7Tyr). This variant is not present in population databases (gnomAD no frequency). This variant has not been reported in the literature in individuals affected with SUN1-related conditions. Algorithms developed to predict the effect of missense changes on protein structure and function are either unavailable or do not agree on the potential impact of this missense change (SIFT: "Deleterious"; PolyPhen-2: "Probably Damaging"; Align-GVGD: "Class C0"). 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.
ClinVar Genomic variation as it relates to human health
NM_001130965.3(SUN1):c.19C>T (p.His7Tyr)
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_001130965.3(SUN1):c.19C>T (p.His7Tyr)
Variation ID: 1979894 Accession: VCV001979894.3
- Type and length
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single nucleotide variant, 1 bp
- Location
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Cytogenetic: 7p22.3 7: 832543 (GRCh38) [ NCBI UCSC ] 7: 872180 (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 Feb 28, 2024 Apr 30, 2022 - HGVS
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... more HGVS ... less HGVSNucleotide Protein Molecular
consequenceNM_001130965.3:c.19C>T MANE Select Help Transcripts from the Matched Annotation from the NCBI and EMBL-EBI (MANE) collaboration.
NP_001124437.1:p.His7Tyr missense NM_001171944.2:c.19C>T NP_001165415.1:p.His7Tyr missense NM_001171945.2:c.82C>T NP_001165416.1:p.His28Tyr missense NM_001171946.2:c.19C>T NP_001165417.1:p.His7Tyr missense NM_001367633.1:c.19C>T NP_001354562.1:p.His7Tyr missense NM_001367634.1:c.19C>T NP_001354563.1:p.His7Tyr missense NM_001367635.1:c.-439C>T 5 prime UTR NM_001367636.1:c.-73-6255C>T intron variant NM_001367637.1:c.-73-6255C>T intron variant NM_001367638.1:c.19C>T NP_001354567.1:p.His7Tyr missense NM_001367639.1:c.-301-9403C>T intron variant NM_001367640.1:c.19C>T NP_001354569.1:p.His7Tyr missense NM_001367641.1:c.19C>T NP_001354570.1:p.His7Tyr missense NM_001367642.1:c.19C>T NP_001354571.1:p.His7Tyr missense NM_001367643.1:c.19C>T NP_001354572.1:p.His7Tyr missense NM_001367644.1:c.-73-6255C>T intron variant NM_001367645.1:c.-73-6255C>T intron variant NM_001367646.1:c.-73-6255C>T intron variant NM_001367647.1:c.-73-6255C>T intron variant NM_001367648.1:c.-73-6255C>T intron variant NM_001367649.1:c.-73-6255C>T intron variant NM_001367651.1:c.297-6255C>T intron variant NM_001367653.1:c.19C>T NP_001354582.1:p.His7Tyr missense NM_001367655.1:c.-73-6255C>T intron variant NM_001367658.1:c.-684-6255C>T intron variant NM_001367660.1:c.-73-6255C>T intron variant NM_001367662.1:c.-73-6255C>T intron variant NM_001367664.1:c.19C>T NP_001354593.1:p.His7Tyr missense NM_001367665.1:c.19C>T NP_001354594.1:p.His7Tyr missense NM_001367666.1:c.-73-6255C>T intron variant NM_001367667.1:c.-73-6255C>T intron variant NM_001367668.1:c.-73-6255C>T intron variant NM_001367669.1:c.19C>T NP_001354598.1:p.His7Tyr missense NM_001367670.1:c.-73-6255C>T intron variant NM_001367671.1:c.-73-6255C>T intron variant NM_001367672.1:c.19C>T NP_001354601.1:p.His7Tyr missense NM_001367673.1:c.-73-6255C>T intron variant NM_001367674.1:c.19C>T NP_001354603.1:p.His7Tyr missense NM_001367675.1:c.19C>T NP_001354604.1:p.His7Tyr missense NM_001367676.1:c.19C>T NP_001354605.1:p.His7Tyr missense NM_001367677.1:c.19C>T NP_001354606.1:p.His7Tyr missense NM_001367678.1:c.19C>T NP_001354607.1:p.His7Tyr missense NM_001367679.1:c.-73-6255C>T intron variant NM_001367680.1:c.-73-6255C>T intron variant NM_001367681.1:c.-73-6255C>T intron variant NM_001367682.1:c.19C>T NP_001354611.1:p.His7Tyr missense NM_001367683.1:c.19C>T NP_001354612.1:p.His7Tyr missense NM_001367684.1:c.-73-6255C>T intron variant NM_001367685.1:c.19C>T NP_001354614.1:p.His7Tyr missense NM_001367686.1:c.-73-6255C>T intron variant NM_001367687.1:c.19C>T NP_001354616.1:p.His7Tyr missense NM_001367688.1:c.19C>T NP_001354617.1:p.His7Tyr missense NM_001367689.1:c.-73-6255C>T intron variant NM_001367690.1:c.19C>T NP_001354619.1:p.His7Tyr missense NM_001367691.1:c.-73-6255C>T intron variant NM_001367692.1:c.19C>T NP_001354621.1:p.His7Tyr missense NM_001367693.1:c.19C>T NP_001354622.1:p.His7Tyr missense NM_001367694.1:c.19C>T NP_001354623.1:p.His7Tyr missense NM_001367695.1:c.19C>T NP_001354624.1:p.His7Tyr missense NM_001367696.1:c.19C>T NP_001354625.1:p.His7Tyr missense NM_001367697.1:c.19C>T NP_001354626.1:p.His7Tyr missense NM_001367698.1:c.19C>T NP_001354627.1:p.His7Tyr missense NM_001367699.1:c.19C>T NP_001354628.1:p.His7Tyr missense NM_001367700.1:c.19C>T NP_001354629.1:p.His7Tyr missense NM_001367701.1:c.-73-6255C>T intron variant NM_001367702.1:c.19C>T NP_001354631.1:p.His7Tyr missense NM_001367703.1:c.19C>T NP_001354632.1:p.His7Tyr missense NM_001367704.1:c.19C>T NP_001354633.1:p.His7Tyr missense NM_001367705.1:c.19C>T NP_001354634.1:p.His7Tyr missense NM_001367706.1:c.-73-6255C>T intron variant NM_025154.6:c.-73-6255C>T intron variant NR_160281.1:n.70C>T non-coding transcript variant NR_160282.1:n.70C>T non-coding transcript variant NR_160283.1:n.70C>T non-coding transcript variant NC_000007.14:g.832543C>T NC_000007.13:g.872180C>T NG_084422.1:g.615C>T - Protein change
- H28Y, H7Y
- Other names
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- Canonical SPDI
- NC_000007.14:832542:C: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 | ||
|---|---|---|---|---|---|---|
| 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. |
|||
| LOC126859921 | - | - | - | GRCh38 | - | 42 |
| SUN1 | - | - |
GRCh38 GRCh37 |
537 | 610 | |
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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Apr 30, 2022 | RCV002756212.3 | |
| Uncertain significance (1) |
criteria provided, single submitter
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Sep 16, 2021 | RCV003491149.2 |
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
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
(Sep 16, 2021)
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criteria provided, single submitter
Method: clinical testing
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not provided
Affected status: unknown
Allele origin:
germline
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Revvity Omics, Revvity
Accession: SCV004237910.1
First in ClinVar: Feb 04, 2024 Last updated: Feb 04, 2024 |
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Uncertain significance
(Apr 30, 2022)
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criteria provided, single submitter
Method: clinical testing
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Emery-Dreifuss muscular dystrophy
Affected status: unknown
Allele origin:
germline
|
Labcorp Genetics (formerly Invitae), Labcorp
Accession: SCV003021985.2
First in ClinVar: Feb 07, 2023 Last updated: Feb 28, 2024 |
Comment:
This sequence change replaces histidine, which is basic and polar, with tyrosine, which is neutral and polar, at codon 7 of the SUN1 protein (p.His7Tyr). … (more)
This sequence change replaces histidine, which is basic and polar, with tyrosine, which is neutral and polar, at codon 7 of the SUN1 protein (p.His7Tyr). This variant is not present in population databases (gnomAD no frequency). This variant has not been reported in the literature in individuals affected with SUN1-related conditions. Algorithms developed to predict the effect of missense changes on protein structure and function are either unavailable or do not agree on the potential impact of this missense change (SIFT: "Deleterious"; PolyPhen-2: "Probably Damaging"; Align-GVGD: "Class C0"). 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)
|
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:
This sequence change replaces histidine, which is basic and polar, with tyrosine, which is neutral and polar, at codon 7 of the SUN1 protein (p.His7Tyr). This variant is not present in population databases (gnomAD no frequency). This variant has not been reported in the literature in individuals affected with SUN1-related conditions. Algorithms developed to predict the effect of missense changes on protein structure and function are either unavailable or do not agree on the potential impact of this missense change (SIFT: "Deleterious"; PolyPhen-2: "Probably Damaging"; Align-GVGD: "Class C0"). 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.
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 Sep 29, 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.