NM_012210.4(TRIM32):c.341del (p.Ser114fs) AND Bardet-Biedl syndrome

Germline classification:: Pathogenic (1 submission)
Last evaluated:: Sep 18, 2023
Review status:: 1 star out of maximum of 4 stars
criteria provided, single submitter

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:: RCV003524396.2

Allele description [Variation Report for NM_012210.4(TRIM32):c.341del (p.Ser114fs)]

NM_012210.4(TRIM32):c.341del (p.Ser114fs)

Genes:

ASTN2:astrotactin 2 [Gene - OMIM - HGNC]
TRIM32:tripartite motif containing 32 [Gene - OMIM - HGNC]

Variant type:

Deletion

Cytogenetic location:

9q33.1

Genomic location:

Preferred name:

NM_012210.4(TRIM32):c.341del (p.Ser114fs)

HGVS:

NC_000009.12:g.116698083del
NG_011619.1:g.15782del
NG_021409.2:g.721975del
NM_001099679.2:c.341del
NM_001365068.1:c.2806+27688delMANE SELECT
NM_001365069.1:c.2794+27688del
NM_001379048.1:c.341del
NM_001379049.1:c.341del
NM_001379050.1:c.341del
NM_012210.4:c.341delMANE SELECT
NM_014010.5:c.2653+27688del
NP_001093149.1:p.Ser114fs
NP_001365977.1:p.Ser114fs
NP_001365978.1:p.Ser114fs
NP_001365979.1:p.Ser114fs
NP_036342.2:p.Ser114Thrfs
NP_036342.2:p.Ser114fs
LRG_211t1:c.341del
LRG_211:g.15782del
LRG_211p1:p.Ser114Thrfs
NC_000009.11:g.119460362del
NM_012210.3:c.341delG

Protein change:

S114fs

Molecular consequence:

NM_001099679.2:c.341del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001379048.1:c.341del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001379049.1:c.341del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001379050.1:c.341del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_012210.4:c.341del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001365068.1:c.2806+27688del - intron variant - [Sequence Ontology: SO:0001627]
NM_001365069.1:c.2794+27688del - intron variant - [Sequence Ontology: SO:0001627]
NM_014010.5:c.2653+27688del - intron variant - [Sequence Ontology: SO:0001627]

Condition(s)

Name:: Bardet-Biedl syndrome (BBS)
Identifiers:: MONDO: MONDO:0015229; MedGen: C0752166; Orphanet: 110; OMIM: PS209900

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KLTH0C03344p [Lachancea thermotolerans CBS 6340]
KLTH0C03344p [Lachancea thermotolerans CBS 6340]
gi|255712177|ref|XP_002552371.1|

Protein

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV004313383	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Pathogenic (Sep 18, 2023)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV004313383

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Pathogenic
(Sep 18, 2023)

germline

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

Citations

PubMed

Sherloc: a comprehensive refinement of the ACMG-AMP variant classification criteria.

Nykamp K, Anderson M, Powers M, Garcia J, Herrera B, Ho YY, Kobayashi Y, Patil N, Thusberg J, Westbrook M; Invitae Clinical Genomics Group., Topper S.

Genet Med. 2017 Oct;19(10):1105-1117. doi: 10.1038/gim.2017.37. Epub 2017 May 11. Erratum in: Genet Med. 2020 Jan;22(1):240. doi: 10.1038/s41436-019-0624-9.

PubMed [citation]

PMID:: 28492532
PMCID:: PMC5632818

Details of each submission

From Labcorp Genetics (formerly Invitae), Labcorp, SCV004313383.1

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

Description

For these reasons, this variant has been classified as Pathogenic. This variant disrupts a region of the TRIM32 protein in which other variant(s) (p.Met370Cysfs*10) have been determined to be pathogenic (Invitae). This suggests that this is a clinically significant region of the protein, and that variants that disrupt it are likely to be disease-causing. This sequence change creates a premature translational stop signal (p.Ser114Thrfs*40) in the TRIM32 gene. While this is not anticipated to result in nonsense mediated decay, it is expected to disrupt the last 540 amino acid(s) of the TRIM32 protein. This variant is not present in population databases (gnomAD no frequency). This variant has not been reported in the literature in individuals affected with TRIM32-related conditions.

#	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

Last Updated: Sep 29, 2024

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