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NM_012210.4(TRIM32):c.389C>T (p.Pro130Leu) AND Bardet-Biedl syndrome

Germline classification:
Uncertain significance (1 submission)
Last evaluated:
Jul 30, 2022
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:
RCV002810782.3

Allele description [Variation Report for NM_012210.4(TRIM32):c.389C>T (p.Pro130Leu)]

NM_012210.4(TRIM32):c.389C>T (p.Pro130Leu)

Genes:
ASTN2:astrotactin 2 [Gene - OMIM - HGNC]
TRIM32:tripartite motif containing 32 [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
9q33.1
Genomic location:
Preferred name:
NM_012210.4(TRIM32):c.389C>T (p.Pro130Leu)
HGVS:
  • NC_000009.12:g.116698131C>T
  • NG_011619.1:g.15830C>T
  • NG_021409.2:g.721927G>A
  • NM_001099679.2:c.389C>T
  • NM_001365068.1:c.2806+27640G>AMANE SELECT
  • NM_001365069.1:c.2794+27640G>A
  • NM_001379048.1:c.389C>T
  • NM_001379049.1:c.389C>T
  • NM_001379050.1:c.389C>T
  • NM_012210.4:c.389C>TMANE SELECT
  • NM_014010.5:c.2653+27640G>A
  • NP_001093149.1:p.Pro130Leu
  • NP_001365977.1:p.Pro130Leu
  • NP_001365978.1:p.Pro130Leu
  • NP_001365979.1:p.Pro130Leu
  • NP_036342.2:p.Pro130Leu
  • NP_036342.2:p.Pro130Leu
  • LRG_211t1:c.389C>T
  • LRG_211:g.15830C>T
  • LRG_211p1:p.Pro130Leu
  • NC_000009.11:g.119460410C>T
  • NM_012210.3:c.389C>T
Protein change:
P130L
Molecular consequence:
  • NM_001365068.1:c.2806+27640G>A - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001365069.1:c.2794+27640G>A - intron variant - [Sequence Ontology: SO:0001627]
  • NM_014010.5:c.2653+27640G>A - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001099679.2:c.389C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001379048.1:c.389C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001379049.1:c.389C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001379050.1:c.389C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_012210.4:c.389C>T - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

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

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV003209655Labcorp Genetics (formerly Invitae), Labcorp
criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))		Uncertain significance
(Jul 30, 2022) 		germlineclinical testing

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

Help

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineunknownnot providednot providednot providednot providednot providedclinical testing

Citations

PubMed

Homozygosity mapping with SNP arrays identifies TRIM32, an E3 ubiquitin ligase, as a Bardet-Biedl syndrome gene (BBS11).

Chiang AP, Beck JS, Yen HJ, Tayeh MK, Scheetz TE, Swiderski RE, Nishimura DY, Braun TA, Kim KY, Huang J, Elbedour K, Carmi R, Slusarski DC, Casavant TL, Stone EM, Sheffield VC.

Proc Natl Acad Sci U S A. 2006 Apr 18;103(16):6287-92. Epub 2006 Apr 10.

PubMed [citation]
PMID:
16606853
PMCID:
PMC1458870

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, SCV003209655.2

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (2)

Description

In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. This variant disrupts the p.Pro130 amino acid residue in TRIM32. Other variant(s) that disrupt this residue have been determined to be pathogenic (PMID: 16606853). This suggests that this residue is clinically significant, and that variants that disrupt this residue are likely to be disease-causing. Algorithms developed to predict the effect of missense changes on protein structure and function output the following: SIFT: "Tolerated"; PolyPhen-2: "Benign"; Align-GVGD: "Class C0". The leucine amino acid residue is found in multiple mammalian species, which suggests that this missense change does not adversely affect protein function. This variant has not been reported in the literature in individuals affected with TRIM32-related conditions. This variant is not present in population databases (gnomAD no frequency). This sequence change replaces proline, which is neutral and non-polar, with leucine, which is neutral and non-polar, at codon 130 of the TRIM32 protein (p.Pro130Leu).

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknownnot providednot providednot providednot providednot providednot providednot provided

Last Updated: Sep 29, 2024