NM_012210.4(TRIM32):c.493C>T (p.Arg165Trp) AND Bardet-Biedl syndrome

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Aug 13, 2021
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:: RCV001352032.6

Allele description [Variation Report for NM_012210.4(TRIM32):c.493C>T (p.Arg165Trp)]

NM_012210.4(TRIM32):c.493C>T (p.Arg165Trp)

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.493C>T (p.Arg165Trp)

HGVS:

NC_000009.12:g.116698235C>T
NG_011619.1:g.15934C>T
NG_021409.2:g.721823G>A
NM_001099679.2:c.493C>T
NM_001365068.1:c.2806+27536G>AMANE SELECT
NM_001365069.1:c.2794+27536G>A
NM_001379048.1:c.493C>T
NM_001379049.1:c.493C>T
NM_001379050.1:c.493C>T
NM_012210.4:c.493C>TMANE SELECT
NM_014010.5:c.2653+27536G>A
NP_001093149.1:p.Arg165Trp
NP_001365977.1:p.Arg165Trp
NP_001365978.1:p.Arg165Trp
NP_001365979.1:p.Arg165Trp
NP_036342.2:p.Arg165Trp
NP_036342.2:p.Arg165Trp
LRG_211t1:c.493C>T
LRG_211:g.15934C>T
LRG_211p1:p.Arg165Trp
NC_000009.11:g.119460514C>T
NM_012210.3:c.493C>T

Protein change:

R165W

Links:

dbSNP: rs1378775801

NCBI 1000 Genomes Browser:

rs1378775801

Molecular consequence:

NM_001365068.1:c.2806+27536G>A - intron variant - [Sequence Ontology: SO:0001627]
NM_001365069.1:c.2794+27536G>A - intron variant - [Sequence Ontology: SO:0001627]
NM_014010.5:c.2653+27536G>A - intron variant - [Sequence Ontology: SO:0001627]
NM_001099679.2:c.493C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001379048.1:c.493C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001379049.1:c.493C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001379050.1:c.493C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_012210.4:c.493C>T - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

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

Recent activity

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MULTISPECIES: CotY/CotZ family spore coat protein [Bacillus]
MULTISPECIES: CotY/CotZ family spore coat protein [Bacillus]
gi|643378769|ref|WP_025207165.1|

Protein
zs03b01.r1 NCI_CGAP_GCB1 Homo sapiens cDNA clone IMAGE:684073 5', mRNA sequence
zs03b01.r1 NCI_CGAP_GCB1 Homo sapiens cDNA clone IMAGE:684073 5', mRNA sequence
gi|1886198|gnl|dbEST|892773|gb|AA25 1|

Nucleotide

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV001546555	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (Aug 13, 2021)	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

SCV001546555

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(Aug 13, 2021)

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, SCV001546555.3

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

Description

This sequence change replaces arginine with tryptophan at codon 165 of the TRIM32 protein (p.Arg165Trp). The arginine residue is moderately conserved and there is a moderate physicochemical difference between arginine and tryptophan. This variant is not present in population databases (ExAC no frequency). This variant has not been reported in the literature in individuals affected with TRIM32-related conditions. Algorithms developed to predict the effect of missense changes on protein structure and function are either unavailable or do not agree on the potential impact of this missense change (SIFT: "Deleterious"; PolyPhen-2: "Benign"; Align-GVGD: "Class C25"). 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.

#	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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