NM_024685.4(BBS10):c.2119_2120del (p.Thr706_Val707insTer) AND Bardet-Biedl syndrome 10

Germline classification:: Pathogenic/Likely pathogenic (5 submissions)
Last evaluated:: Feb 27, 2024
Review status:: 2 stars out of maximum of 4 stars
criteria provided, multiple submitters, no conflicts

Somatic classification of clinical impact:: None
Review status:: (0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided

Somatic classification of oncogenicity:: None
Review status:: (0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided

Record status:: current
Accession:: RCV000665753.9

Allele description [Variation Report for NM_024685.4(BBS10):c.2119_2120del (p.Thr706_Val707insTer)]

NM_024685.4(BBS10):c.2119_2120del (p.Thr706_Val707insTer)

Gene:

BBS10:Bardet-Biedl syndrome 10 [Gene - OMIM - HGNC]

Variant type:

Deletion

Cytogenetic location:

12q21.2

Genomic location:

Preferred name:

NM_024685.4(BBS10):c.2119_2120del (p.Thr706_Val707insTer)

HGVS:

NC_000012.11:g.76739645_76739646del
NC_000012.12:g.76345866_76345867del
NG_016357.1:g.7577_7578del
NM_024685.4:c.2119_2120delMANE SELECT
NP_078961.3:p.Thr706_Val707insTer
LRG_1255t1:c.2119_2120del
LRG_1255:g.7577_7578del
LRG_1255p1:p.Thr706_Val707insTer
NC_000012.11:g.76739645_76739646del
NC_000012.11:g.76739645_76739646delAC
NC_000012.11:g.76739646_76739647del
NM_024685.3:c.2119_2120del
NM_024685.3:c.2119_2120delGT
p.Val707X

Links:

dbSNP: rs775950661

NCBI 1000 Genomes Browser:

rs775950661

Molecular consequence:

NM_024685.4:c.2119_2120del - nonsense - [Sequence Ontology: SO:0001587]

Condition(s)

Name:: Bardet-Biedl syndrome 10 (BBS10)
Identifiers:: MONDO: MONDO:0014438; MedGen: C1859568; Orphanet: 110; OMIM: 615987

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000789921	Counsyl	no assertion criteria provided	Pathogenic (Feb 27, 2017)	unknown	clinical testing	PubMed (5) [See all records that cite these PMIDs] 16582908, 22773737, 21157496, 21209035, 27659767
SCV001445876	Rady Children's Institute for Genomic Medicine, Rady Children's Hospital San Diego	criteria provided, single submitter (ACMG Guidelines, 2015)	Pathogenic (Oct 10, 2019)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]
SCV002091737	Natera, Inc.	no assertion criteria provided	Pathogenic (Jan 18, 2020)	germline	clinical testing
SCV003824641	Revvity Omics, Revvity	criteria provided, single submitter (ACMG Guidelines, 2015)	Likely pathogenic (Jun 1, 2023)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]
SCV004217416	Baylor Genetics	criteria provided, single submitter (ACMG Guidelines, 2015)	Pathogenic (Feb 27, 2024)	unknown	clinical testing	PubMed (1) [See all records that cite this PMID]

Help

Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	germline	unknown	not provided	not provided	not provided	not provided	not provided	clinical testing
not provided	germline	yes	not provided	not provided	not provided	not provided	not provided	clinical testing
not provided	unknown	unknown	not provided	not provided	not provided	not provided	not provided	clinical testing

Citations

PubMed

BBS10 encodes a vertebrate-specific chaperonin-like protein and is a major BBS locus.

Stoetzel C, Laurier V, Davis EE, Muller J, Rix S, Badano JL, Leitch CC, Salem N, Chouery E, Corbani S, Jalk N, Vicaire S, Sarda P, Hamel C, Lacombe D, Holder M, Odent S, Holder S, Brooks AS, Elcioglu NH, Silva ED, Rossillion B, et al.

Nat Genet. 2006 May;38(5):521-4. Epub 2006 Apr 2. Erratum in: Nat Genet. 2006 Jun;38(6):727. Da Silva, Eduardo [corrected to Silva, Eduardo D].

PubMed [citation]

PMID:: 16582908

Targeted high-throughput sequencing for diagnosis of genetically heterogeneous diseases: efficient mutation detection in Bardet-Biedl and Alström syndromes.

Redin C, Le Gras S, Mhamdi O, Geoffroy V, Stoetzel C, Vincent MC, Chiurazzi P, Lacombe D, Ouertani I, Petit F, Till M, Verloes A, Jost B, Chaabouni HB, Dollfus H, Mandel JL, Muller J.

J Med Genet. 2012 Aug;49(8):502-12. doi: 10.1136/jmedgenet-2012-100875. Epub 2012 Jul 7.

PubMed [citation]

PMID:: 22773737
PMCID:: PMC3436454

See all PubMed Citations (6)

Details of each submission

From Counsyl, SCV000789921.2

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (5)

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	unknown	unknown	not provided	not provided	not provided		not provided	not provided	not provided	not provided

From Rady Children's Institute for Genomic Medicine, Rady Children's Hospital San Diego, SCV001445876.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (1)

Description

This frameshifting variant in exon 2 of 2 introduces a premature stop codon and is therefore predicted to result in loss of normal protein function. While this is not anticipated to result in nonsense mediated decay, it is expected to delete the last 17 amino acids of the BBS10 protein. This variant has been previously reported as a compound heterozygous or homozygous change in patients with Bardet-Biedl Syndrome 10 (PMID: 16582908, 25982971, 22773737, 27486776, 20472660). The ClinVar database contains an entry for this variant (Variation ID: 406221). It is present in the heterozygous state in the gnomAD population database at a frequency of 0.006% (17/282614) and thus is presumed to be rare. Based on the available evidence, the c.2119_2120del (p.Val707Ter) variant is classified as Pathogenic.

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	yes	not provided	not provided	not provided		not provided	not provided	not provided	not provided

From Natera, Inc., SCV002091737.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	not provided

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	unknown	not provided	not provided	not provided		not provided	not provided	not provided	not provided

From Revvity Omics, Revvity, SCV003824641.2

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (1)

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	unknown	not provided	not provided	not provided		not provided	not provided	not provided	not provided

From Baylor Genetics, SCV004217416.2

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (1)

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	unknown	unknown	not provided	not provided	not provided		not provided	not provided	not provided	not provided

Last Updated: Sep 29, 2024

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