ClinVar Genomic variation as it relates to human health
NM_198428.3(BBS9):c.1877_1880del (p.Lys626fs)
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.1877_1880del (p.Lys626fs)
Variation ID: 2662 Accession: VCV000002662.18
- Type and length
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Deletion, 4 bp
- Location
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Cytogenetic: 7p14.3 7: 33383752-33383755 (GRCh38) [ NCBI UCSC ] 7: 33423364-33423367 (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 Mar 8, 2017 Aug 25, 2024 Mar 12, 2024 - HGVS
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Nucleotide Protein Molecular
consequenceNM_198428.3:c.1877_1880del MANE Select Help Transcripts from the Matched Annotation from the NCBI and EMBL-EBI (MANE) collaboration.
NP_940820.1:p.Lys626fs frameshift NM_001033604.2:c.1772_1775del NP_001028776.1:p.Lys591fs frameshift NM_001033605.2:c.1862_1865del NP_001028777.1:p.Lys621fs frameshift NM_001348036.1:c.1877_1880del NP_001334965.1:p.Lys626fs frameshift NM_001348037.3:c.1511_1514del NP_001334966.1:p.Lys504fs frameshift NM_001348038.3:c.1604_1607del NP_001334967.1:p.Lys535fs frameshift NM_001348039.3:c.1499_1502del NP_001334968.1:p.Lys500fs frameshift NM_001348040.3:c.1757_1760del NP_001334969.1:p.Lys586fs frameshift NM_001348041.4:c.1877_1880del NP_001334970.1:p.Lys626fs frameshift NM_001348042.3:c.1742_1745del NP_001334971.1:p.Lys581fs frameshift NM_001348043.3:c.1877_1880del NP_001334972.1:p.Lys626fs frameshift NM_001348044.3:c.1406_1409del NP_001334973.1:p.Lys469fs frameshift NM_001348045.3:c.1511_1514del NP_001334974.1:p.Lys504fs frameshift NM_001348046.3:c.1511_1514del NP_001334975.1:p.Lys504fs frameshift NM_001362679.1:c.1877_1880del NP_001349608.1:p.Lys626fs frameshift NM_014451.4:c.1757_1760del NP_055266.2:p.Lys586fs frameshift NM_198428.2:c.1877_1880del NR_145411.1:n.2156_2159del non-coding transcript variant NR_145412.1:n.2348_2351del non-coding transcript variant NR_145413.3:n.2510_2513del non-coding transcript variant NC_000007.14:g.33383753_33383756del NC_000007.13:g.33423365_33423368del NG_009306.2:g.259510_259513del - Protein change
- K504fs, K581fs, K500fs, K535fs, K621fs, K626fs, K586fs, K591fs, K469fs
- Other names
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- Canonical SPDI
- NC_000007.14:33383751:AAACA: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
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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
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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BBS9 | - | - |
GRCh38 GRCh37 |
1057 | 1093 |
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. |
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Pathogenic (4) |
criteria provided, multiple submitters, no conflicts
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Mar 12, 2024 | RCV000002781.11 | |
Pathogenic (4) |
criteria provided, multiple submitters, no conflicts
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Aug 28, 2023 | RCV000433738.6 | |
Pathogenic (1) |
criteria provided, single submitter
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Jan 19, 2024 | RCV000614851.8 | |
Pathogenic (2) |
criteria provided, single submitter
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Jan 6, 2016 | RCV000709632.2 | |
BBS9-related disorder
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Pathogenic (1) |
criteria provided, single submitter
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Dec 8, 2023 | RCV003421896.5 |
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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Pathogenic
(Jan 19, 2024)
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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: SCV000832371.6
First in ClinVar: Oct 10, 2018 Last updated: Feb 14, 2024 |
Comment:
This sequence change creates a premature translational stop signal (p.Lys626Argfs*22) 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.Lys626Argfs*22) 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 (rs774006614, gnomAD 0.01%). This premature translational stop signal has been observed in individuals with Bardet-Biedl syndrome (PMID: 16380913). It has also been observed to segregate with disease in related individuals. ClinVar contains an entry for this variant (Variation ID: 2662). For these reasons, this variant has been classified as Pathogenic. (less)
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Pathogenic
(Dec 08, 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: SCV004116747.2
First in ClinVar: Nov 20, 2023 Last updated: Mar 16, 2024 |
Comment:
The BBS9 c.1877_1880delAACA variant is predicted to result in a frameshift and premature protein termination (p.Lys626Argfs*22). This variant has been reported in the homozygous and … (more)
The BBS9 c.1877_1880delAACA variant is predicted to result in a frameshift and premature protein termination (p.Lys626Argfs*22). This variant has been reported in the homozygous and compound heterozygous states in individuals with Bardet-Biedl syndrome (Nishimura et al. 2005. PubMed ID: 16380913; Meyer et al. 2022. PubMed ID: 35112343). This variant is reported in 0.011% of alleles in individuals of European (Non-Finnish) descent in gnomAD. Frameshift variants in BBS9 are expected to be pathogenic. Given the evidence, we interpret this variant as pathogenic. (less)
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Pathogenic
(Dec 05, 2016)
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criteria provided, single submitter
Method: clinical testing
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not provided
Affected status: not provided
Allele origin:
germline
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Center for Pediatric Genomic Medicine, Children's Mercy Hospital and Clinics
Accession: SCV000511853.1
First in ClinVar: Mar 08, 2017 Last updated: Mar 08, 2017 |
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Pathogenic
(Jan 06, 2016)
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criteria provided, single submitter
Method: clinical testing
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Bardet-Biedl syndrome 1
Affected status: yes
Allele origin:
germline
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Genome Diagnostics Laboratory, University Medical Center Utrecht
Study: VKGL Data-share Consensus
Accession: SCV000743768.1 First in ClinVar: Apr 09, 2018 Last updated: Apr 09, 2018 |
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Pathogenic
(Dec 20, 2022)
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criteria provided, single submitter
Method: clinical testing
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Bardet-Biedl syndrome 9
(Autosomal recessive inheritance)
Affected status: yes
Allele origin:
germline
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Institute of Medical Genetics and Applied Genomics, University Hospital Tübingen
Accession: SCV002765131.1
First in ClinVar: Dec 24, 2022 Last updated: Dec 24, 2022 |
Clinical Features:
Rod-cone dystrophy (present) , Optic atrophy (present) , Leber optic atrophy (present) , Intellectual disability (present)
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Pathogenic
(Feb 18, 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:
unknown
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Fulgent Genetics, Fulgent Genetics
Accession: SCV002811476.1
First in ClinVar: Dec 31, 2022 Last updated: Dec 31, 2022 |
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Pathogenic
(Mar 12, 2024)
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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: SCV004214186.2
First in ClinVar: Dec 30, 2023 Last updated: Jun 17, 2024 |
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Pathogenic
(Aug 28, 2023)
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criteria provided, single submitter
Method: clinical testing
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not provided
Affected status: yes
Allele origin:
germline
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Clinical Genetics Laboratory, Skane University Hospital Lund
Accession: SCV005199071.1
First in ClinVar: Aug 25, 2024 Last updated: Aug 25, 2024 |
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Pathogenic
(Dec 01, 2005)
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no assertion criteria provided
Method: literature only
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BARDET-BIEDL SYNDROME 9
Affected status: not provided
Allele origin:
germline
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OMIM
Accession: SCV000022939.4
First in ClinVar: Apr 04, 2013 Last updated: Jun 24, 2017 |
Comment on evidence:
For discussion of the 4-bp deletion (c.1877_1880delAACA, NM_198428) in the BBS9 gene that was found in compound heterozygous state in a patient with Bardet-Biedl syndrome-9 … (more)
For discussion of the 4-bp deletion (c.1877_1880delAACA, NM_198428) in the BBS9 gene that was found in compound heterozygous state in a patient with Bardet-Biedl syndrome-9 (BBS9; 615986) by Nishimura et al. (2005), see 607968.0006. (less)
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Pathogenic
(-)
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no assertion criteria provided
Method: clinical testing
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Bardet-Biedl syndrome 1
Affected status: yes
Allele origin:
germline
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Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen
Study: VKGL Data-share Consensus
Accession: SCV000734550.1 First in ClinVar: Apr 09, 2018 Last updated: Apr 09, 2018 |
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Pathogenic
(-)
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no assertion criteria provided
Method: clinical testing
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not provided
Affected status: yes
Allele origin:
germline
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Joint Genome Diagnostic Labs from Nijmegen and Maastricht, Radboudumc and MUMC+
Additional submitter:
Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen
Study: VKGL Data-share Consensus
Accession: SCV001955942.1 First in ClinVar: Oct 02, 2021 Last updated: Oct 02, 2021 |
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Pathogenic
(-)
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no assertion criteria provided
Method: clinical testing
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not provided
Affected status: yes
Allele origin:
germline
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Genome Diagnostics Laboratory, Amsterdam University Medical Center
Study: VKGL Data-share Consensus
Accession: SCV001809306.1 First in ClinVar: Aug 25, 2021 Last updated: Aug 25, 2021 |
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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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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 rs606231137 ...
HelpRecord last updated Aug 25, 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.