ClinVar Genomic variation as it relates to human health
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- Interpretation:
-
risk factor
- Review status:
- no assertion criteria provided
- Submissions:
- 1
- First in ClinVar:
- Sep 1, 2017
- Most recent Submission:
- Sep 1, 2017
- Last evaluated:
- Apr 1, 2005
- Accession:
- VCV000004649.1
- Variation ID:
- 4649
- Description:
- single nucleotide variant
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NM_001304561.2(BTNL2):c.1078= (p.Ser360=)
- Allele ID
- 19688
- Variant type
- single nucleotide variant
- Variant length
- -
- Cytogenetic location
- 6p21.32
- Genomic location
- 6: 32396039 (GRCh38) GRCh38 UCSC
- 6: 32363816 (GRCh37) GRCh37 UCSC
- HGVS
-
... more HGVS ... less HGVSNucleotide Protein Molecular
consequenceNM_001304561.2:c.1078= MANE Select NP_001291490.1:p.Ser360= no sequence alteration NM_001304561.1:c.1078A= no sequence alteration NC_000006.12:g.32396039= NC_000006.11:g.32363816= NG_054759.1:g.17841= - Protein change
- -
- Other names
- IVS5AS, G-A, -1 (rs2076530)
- Canonical SPDI
- NC_000006.12:32396038:T:T
- Functional consequence
- -
- Global minor allele frequency (GMAF)
- 0.38698 (C)
- Allele frequency
- Exome Aggregation Consortium (ExAC) 0.57400
- Trans-Omics for Precision Medicine (TOPMed) 0.59802
- The Genome Aggregation Database (gnomAD) 0.60050
- NHLBI Exome Sequencing Project (ESP) Exome Variant Server 0.60301
- Trans-Omics for Precision Medicine (TOPMed) 0.60623
- The Genome Aggregation Database (gnomAD) 0.60813
- The Genome Aggregation Database (gnomAD), exomes 0.57708
- 1000 Genomes Project 0.61302
- Links
- ClinGen: CA16044112
- OMIM: 606000.0001
- dbSNP: rs2076530
- VarSome
- Comment on variant
- Figure 3 in the paper by Valentonyte et al. 2005, (PubMed 15735647) asserts that the A allele is the risk allele. That is the current reference sequence.
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Aggregate interpretations per condition
| Interpreted condition | Interpretation | Number of submissions | Review status | Last evaluated | Variation/condition record |
|---|---|---|---|---|---|
| risk factor | 1 | no assertion criteria provided | Apr 1, 2005 | RCV000004912.3 |
Submitted interpretations and evidence
Help| Interpretation (Last evaluated) |
Review status (Assertion criteria) |
Condition (Inheritance) |
Submitter | More information | |
|---|---|---|---|---|---|
|
risk factor
(Apr 01, 2005)
|
no assertion criteria provided
Method: literature only
|
Affected status: not provided
Allele origin:
germline
|
OMIM
Accession: SCV000025088.2
First in ClinVar: Apr 04, 2013 Last updated: Sep 01, 2017 |
Comment on evidence:
In a study of 947 independent cases of familial and sporadic sarcoidosis (SS2; 612387), Valentonyte et al. (2005) identified a G-to-A transition at position -1 … (more)
In a study of 947 independent cases of familial and sporadic sarcoidosis (SS2; 612387), Valentonyte et al. (2005) identified a G-to-A transition at position -1 of a splice donor site (rs2076530) in the BTNL2 gene. The change resulted in the use of an alternative splice site located 4 bp upstream. The loss of 4 bases from the cDNA transcribed from the A allele resulted in a frameshift and a premature stop in the downstream exon. In the corresponding protein product, the 118 C-terminal residues in the nontruncated protein were replaced by 5 different amino acids. The mutant protein lacks the C-terminal IgC domain and transmembrane helix, thereby disrupting localization of the protein. (less)
|
Functional evidence
Help| 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. |
Citations for this variant
Help| Title | Author | Journal | Year | Link |
|---|---|---|---|---|
| Sarcoidosis is associated with a truncating splice site mutation in BTNL2. | Valentonyte R | Nature genetics | 2005 | PMID: 15735647 |
Text-mined citations for rs2076530...
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 Mar 26, 2023