NM_024685.4(BBS10):c.1337_1338del (p.Phe446fs) AND Bardet-Biedl syndrome 10

Germline classification:: Pathogenic/Likely pathogenic (2 submissions)
Last evaluated:: Aug 6, 2018
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:: RCV001251482.5

Allele description [Variation Report for NM_024685.4(BBS10):c.1337_1338del (p.Phe446fs)]

NM_024685.4(BBS10):c.1337_1338del (p.Phe446fs)

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.1337_1338del (p.Phe446fs)

HGVS:

NC_000012.12:g.76346650_76346651del
NG_016357.1:g.6795_6796del
NM_024685.4:c.1337_1338delMANE SELECT
NP_078961.3:p.Phe446fs
LRG_1255t1:c.1337_1338del
LRG_1255:g.6795_6796del
LRG_1255p1:p.Phe446fs
NC_000012.11:g.76740430_76740431del
NM_024685.3:c.1337_1338delTT
NM_024685.4:c.1337_1338delTTMANE SELECT

Protein change:

F446fs

Links:

dbSNP: rs1389599028

NCBI 1000 Genomes Browser:

rs1389599028

Molecular consequence:

NM_024685.4:c.1337_1338del - frameshift variant - [Sequence Ontology: SO:0001589]

Condition(s)

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

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EST241186 Normalized rat brain, Bento Soares Rattus sp. cDNA clone RBRED85 3' end, mRNA sequence
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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV001427135	Victorian Clinical Genetics Services, Murdoch Childrens Research Institute	criteria provided, single submitter (ACMG Guidelines, 2015)	Likely pathogenic (Aug 6, 2018)	unknown	clinical testing	PubMed (1) [See all records that cite this PMID]
SCV002053979	Kasturba Medical College, Manipal, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, India	criteria provided, single submitter (ACMG Guidelines, 2015)	Pathogenic	inherited	clinical testing	PubMed (2) [See all records that cite these PMIDs] 30408610, 25741868

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV001427135

Victorian Clinical Genetics Services, Murdoch Childrens Research Institute

criteria provided, single submitter

(ACMG Guidelines, 2015)

Likely pathogenic
(Aug 6, 2018)

unknown

clinical testing

PubMed (1)
[See all records that cite this PMID]

SCV002053979

Kasturba Medical College, Manipal, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, India

criteria provided, single submitter

(ACMG Guidelines, 2015)

Pathogenic

inherited

clinical testing

PubMed (2)
[See all records that cite these PMIDs]

Help

Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	inherited	yes	not provided	not provided	not provided	3	not provided	clinical testing
not provided	unknown	yes	not provided	not provided	not provided	not provided	not provided	clinical testing

Citations

PubMed

Phenotyping and genotyping of skeletal dysplasias: Evolution of a center and a decade of experience in India.

Uttarilli A, Shah H, Bhavani GS, Upadhyai P, Shukla A, Girisha KM.

Bone. 2019 Mar;120:204-211. doi: 10.1016/j.bone.2018.10.026. Epub 2018 Nov 6.

PubMed [citation]

PMID:: 30408610

Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology.

Richards S, Aziz N, Bale S, Bick D, Das S, Gastier-Foster J, Grody WW, Hegde M, Lyon E, Spector E, Voelkerding K, Rehm HL; ACMG Laboratory Quality Assurance Committee..

Genet Med. 2015 May;17(5):405-24. doi: 10.1038/gim.2015.30. Epub 2015 Mar 5.

PubMed [citation]

PMID:: 25741868
PMCID:: PMC4544753

Details of each submission

From Victorian Clinical Genetics Services, Murdoch Childrens Research Institute, SCV001427135.2

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

Description

A homozygous frameshift deletion variant, NM_024685.3(BBS10):c.1337_1338delTT, has been identified in exon 2 of 2 of the BBS10 gene. This deletion is predicted to create a frameshift starting at amino acid position 446, introducing a stop codon 3 residues downstream (NP_078961.3(BBS10):p.(Phe446Tyrfs*3)). This variant is predicted to result in loss of protein function through truncation (although no known functional domains are affected). However, loss of function via NMD has not been excluded. The variant is present in the gnomAD database at a frequency of 0.0004% (1 heterozygote). This variant has not been previously reported in clinical cases. Multiple truncating mutations downstream of this variant have also been shown to cause Bardet-Biedl syndrome 10 (ClinVar, HGMD). Based on the information available at the time of curation, this variant has been classified as LIKELY PATHOGENIC.

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

From Kasturba Medical College, Manipal, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, India, SCV002053979.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (2)

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	inherited	yes	3	not provided	not provided		not provided	not provided	not provided	not provided

Last Updated: Feb 25, 2023

ClinVar

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