NM_012210.4(TRIM32):c.388C>T (p.Pro130Ser) AND Bardet-Biedl syndrome

Germline classification:: Pathogenic (1 submission)
Last evaluated:: Dec 12, 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:: RCV000199127.9

Allele description [Variation Report for NM_012210.4(TRIM32):c.388C>T (p.Pro130Ser)]

NM_012210.4(TRIM32):c.388C>T (p.Pro130Ser)

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.388C>T (p.Pro130Ser)

HGVS:

NC_000009.12:g.116698130C>T
NG_011619.1:g.15829C>T
NG_021409.2:g.721928G>A
NM_001099679.2:c.388C>T
NM_001365068.1:c.2806+27641G>AMANE SELECT
NM_001365069.1:c.2794+27641G>A
NM_001379048.1:c.388C>T
NM_001379049.1:c.388C>T
NM_001379050.1:c.388C>T
NM_012210.4:c.388C>TMANE SELECT
NM_014010.5:c.2653+27641G>A
NP_001093149.1:p.Pro130Ser
NP_001365977.1:p.Pro130Ser
NP_001365978.1:p.Pro130Ser
NP_001365979.1:p.Pro130Ser
NP_036342.2:p.Pro130Ser
NP_036342.2:p.Pro130Ser
LRG_211t1:c.388C>T
LRG_211:g.15829C>T
LRG_211p1:p.Pro130Ser
NC_000009.11:g.119460409C>T
NM_012210.3:c.388C>T
Q13049:p.Pro130Ser

Protein change:

P130S; PRO130SER

Links:

UniProtKB: Q13049#VAR_038807; OMIM: 602290.0002; dbSNP: rs111033571

NCBI 1000 Genomes Browser:

rs111033571

Molecular consequence:

NM_001365068.1:c.2806+27641G>A - intron variant - [Sequence Ontology: SO:0001627]
NM_001365069.1:c.2794+27641G>A - intron variant - [Sequence Ontology: SO:0001627]
NM_014010.5:c.2653+27641G>A - intron variant - [Sequence Ontology: SO:0001627]
NM_001099679.2:c.388C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001379048.1:c.388C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001379049.1:c.388C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001379050.1:c.388C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_012210.4:c.388C>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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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000253915	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Pathogenic (Dec 12, 2023)	germline	clinical testing	PubMed (2) [See all records that cite these PMIDs] 16606853, 28492532

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000253915

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Pathogenic
(Dec 12, 2023)

germline

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	germline	unknown	not provided	not provided	not provided	not provided	not provided	clinical 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, SCV000253915.6

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

Description

This sequence change replaces proline, which is neutral and non-polar, with serine, which is neutral and polar, at codon 130 of the TRIM32 protein (p.Pro130Ser). This variant is present in population databases (rs111033571, gnomAD 0.002%). This missense change has been observed in individual(s) with Bardet‚ÄìBiedl syndrome (PMID: 16606853). It has also been observed to segregate with disease in related individuals. ClinVar contains an entry for this variant (Variation ID: 7351). An algorithm developed to predict the effect of missense changes on protein structure and function (PolyPhen-2) suggests that this variant¬†is likely to be tolerated. Experimental studies have shown that this missense change affects TRIM32 function (PMID: 16606853). For these reasons, this variant has been classified as Pathogenic.

#	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: Oct 13, 2024

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