ClinVar Genomic variation as it relates to human health
NM_198428.3(BBS9):c.310del (p.Cys104fs)
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.
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.
No data submitted for somatic clinical impact
No data submitted for oncogenicity
Variant Details
- Identifiers
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NM_198428.3(BBS9):c.310del (p.Cys104fs)
Variation ID: 462970 Accession: VCV000462970.10
- Type and length
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Deletion, 1 bp
- Location
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Cytogenetic: 7p14.3 7: 33155682 (GRCh38) [ NCBI UCSC ] 7: 33195294 (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 Dec 26, 2017 Feb 20, 2024 Dec 25, 2023 - HGVS
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Nucleotide Protein Molecular
consequenceNM_198428.3:c.310del MANE Select Help Transcripts from the Matched Annotation from the NCBI and EMBL-EBI (MANE) collaboration.
NP_940820.1:p.Cys104fs frameshift NM_001033604.2:c.310del NP_001028776.1:p.Cys104fs frameshift NM_001033605.2:c.310del NP_001028777.1:p.Cys104fs frameshift NM_001348036.1:c.310del NP_001334965.1:p.Cys104fs frameshift NM_001348037.3:c.-39+2833del intron variant NM_001348038.3:c.37del NP_001334967.1:p.Cys13fs frameshift NM_001348039.3:c.37del NP_001334968.1:p.Cys13fs frameshift NM_001348040.3:c.310del NP_001334969.1:p.Cys104fs frameshift NM_001348041.4:c.310del NP_001334970.1:p.Cys104fs frameshift NM_001348042.3:c.175del NP_001334971.1:p.Cys59fs frameshift NM_001348043.3:c.310del NP_001334972.1:p.Cys104fs frameshift NM_001348044.3:c.-38-21794del intron variant NM_001348045.3:c.-39+2833del intron variant NM_001348046.3:c.-38-21794del intron variant NM_001362679.1:c.310del NP_001349608.1:p.Cys104fs frameshift NM_014451.4:c.310del NP_055266.2:p.Cys104fs frameshift NM_198428.2:c.310del NR_145411.1:n.589del non-coding transcript variant NR_145412.1:n.589del non-coding transcript variant NR_145413.3:n.799del non-coding transcript variant NC_000007.14:g.33155684del NC_000007.13:g.33195296del NG_009306.2:g.31441del - Protein change
- C104fs, C13fs, C59fs
- Other names
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- Canonical SPDI
- NC_000007.14:33155681:TTT:TT
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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
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The frequency of the allele represented by this VCV record.
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Genes
Gene | OMIM | ClinGen Gene Dosage Sensitivity Curation |
Variation Viewer
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Links to Variation Viewer, a genome browser to view variation data from NCBI databases. |
Related variants | ||
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HI score
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The haploinsufficiency score for the gene, curated by ClinGen’s Dosage Sensitivity Curation task team. |
TS score
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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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BBS9 | - | - |
GRCh38 GRCh37 |
1030 | 1065 |
Conditions - Germline
Condition
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The condition for this variant-condition (RCV) record in ClinVar. |
Classification
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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
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The most recent date that a submitter evaluated this variant for the condition. |
Variation/condition record
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The RCV accession number, with most recent version number, for the variant-condition record, with a link to the RCV web page. |
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Pathogenic (1) |
criteria provided, single submitter
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Dec 25, 2023 | RCV000548595.6 | |
Pathogenic (3) |
criteria provided, multiple submitters, no conflicts
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Oct 11, 2023 | RCV002248767.3 | |
Likely pathogenic (1) |
criteria provided, single submitter
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Aug 11, 2023 | RCV003419945.4 |
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
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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
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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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Pathogenic
(May 04, 2022)
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criteria provided, single submitter
Method: clinical testing
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Bardet-Biedl syndrome 9
Affected status: unknown
Allele origin:
germline
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Mendelics
Accession: SCV002518563.1
First in ClinVar: May 28, 2022 Last updated: May 28, 2022 |
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Pathogenic
(Dec 27, 2021)
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criteria provided, single submitter
Method: clinical testing
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Bardet-Biedl syndrome 9
Affected status: unknown
Allele origin:
unknown
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Fulgent Genetics, Fulgent Genetics
Accession: SCV002780552.1
First in ClinVar: Dec 31, 2022 Last updated: Dec 31, 2022 |
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Likely pathogenic
(Aug 11, 2023)
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criteria provided, single submitter
Method: clinical testing
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BBS9-related condition
Affected status: unknown
Allele origin:
germline
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PreventionGenetics, part of Exact Sciences
Accession: SCV004116490.1
First in ClinVar: Nov 20, 2023 Last updated: Nov 20, 2023 |
Comment:
The BBS9 c.310delT variant is predicted to result in a frameshift and premature protein termination (p.Cys104Valfs*20). The c.310del variant has been reported, along with a … (more)
The BBS9 c.310delT variant is predicted to result in a frameshift and premature protein termination (p.Cys104Valfs*20). The c.310del variant has been reported, along with a variant of uncertain significance, in a teenage patient with obesity (Supplementary Table 3, Kleinendorst et al. 2018. PubMed ID: 29970488). This variant was also reported with another BBS9 frameshift variant in a patient with Bardet-Biedl syndrome (K131 in Zacchia et al. 2021. PubMed ID: 33964006). This variant is reported in 0.051% of alleles in individuals of Latino descent in gnomAD (http://gnomad.broadinstitute.org/variant/7-33195293-CT-C). Frameshift variants in BBS9 are expected to be pathogenic for autosomal recessive Bardet-Biedl syndrome (Khan et al. 2016. PubMed ID: 26846096; Supplementary Table 3, Shaheen et al. 2016. PubMed ID: 27894351; OMIM: #615986). This variant is interpreted as likely pathogenic. (less)
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Pathogenic
(Oct 11, 2023)
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criteria provided, single submitter
Method: clinical testing
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Bardet-Biedl syndrome 9
Affected status: unknown
Allele origin:
unknown
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Baylor Genetics
Accession: SCV004214191.1
First in ClinVar: Dec 30, 2023 Last updated: Dec 30, 2023 |
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Pathogenic
(Dec 25, 2023)
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criteria provided, single submitter
Method: clinical testing
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Bardet-Biedl syndrome
Affected status: unknown
Allele origin:
germline
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Invitae
Accession: SCV000636556.6
First in ClinVar: Dec 26, 2017 Last updated: Feb 20, 2024 |
Comment:
This sequence change creates a premature translational stop signal (p.Cys104Valfs*20) in the BBS9 gene. It is expected to result in an absent or disrupted protein … (more)
This sequence change creates a premature translational stop signal (p.Cys104Valfs*20) in the BBS9 gene. It is expected to result in an absent or disrupted protein product. Loss-of-function variants in BBS9 are known to be pathogenic (PMID: 16380913, 20177705). This variant is present in population databases (rs777498165, gnomAD 0.05%). This premature translational stop signal has been observed in individual(s) with obesity (PMID: 29970488). ClinVar contains an entry for this variant (Variation ID: 462970). For these reasons, this variant has been classified as Pathogenic. (less)
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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. |
Citations for germline classification of this variant
HelpTitle | Author | Journal | Year | Link |
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Genetic obesity: next-generation sequencing results of 1230 patients with obesity. | Kleinendorst L | Journal of medical genetics | 2018 | PMID: 29970488 |
Identification of 28 novel mutations in the Bardet-Biedl syndrome genes: the burden of private mutations in an extensively heterogeneous disease. | Muller J | Human genetics | 2010 | PMID: 20177705 |
Comparative genomics and gene expression analysis identifies BBS9, a new Bardet-Biedl syndrome gene. | Nishimura DY | American journal of human genetics | 2005 | PMID: 16380913 |
Text-mined citations for rs747388658 ...
HelpRecord last updated Mar 11, 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.