NM_001160372.4(TRAPPC9):c.3149G>A (p.Arg1050Gln) AND not provided

Germline classification:: Likely benign (2 submissions)
Last evaluated:: Jan 21, 2024
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:: RCV001815322.27

Allele description [Variation Report for NM_001160372.4(TRAPPC9):c.3149G>A (p.Arg1050Gln)]

NM_001160372.4(TRAPPC9):c.3149G>A (p.Arg1050Gln)

Gene:

TRAPPC9:trafficking protein particle complex subunit 9 [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

8q24.3

Genomic location:

Preferred name:

NM_001160372.4(TRAPPC9):c.3149G>A (p.Arg1050Gln)

HGVS:

NC_000008.11:g.139732109C>T
NG_016478.3:g.731471G>A
NM_001160372.4:c.3149G>AMANE SELECT
NM_001321646.2:c.3122G>A
NM_001374682.1:c.3170G>A
NM_001374683.1:c.3038G>A
NM_001374684.1:c.3005G>A
NM_031466.8:c.3149G>A
NP_001153844.1:p.Arg1050Gln
NP_001308575.1:p.Arg1041Gln
NP_001361611.1:p.Arg1057Gln
NP_001361612.1:p.Arg1013Gln
NP_001361613.1:p.Arg1002Gln
NP_113654.4:p.Arg1148Gln
NP_113654.5:p.Arg1050Gln
LRG_1041t1:c.3149G>A
LRG_1041t2:c.3149G>A
LRG_1041:g.731471G>A
LRG_1041p1:p.Arg1050Gln
LRG_1041p2:p.Arg1050Gln
NC_000008.10:g.140744352C>T
NG_016478.2:g.731471G>A
NM_031466.5:c.3443G>A
NM_031466.6:c.3443G>A
NM_031466.7:c.3443G>A
NR_164662.1:n.3311G>A

Protein change:

R1002Q

Links:

dbSNP: rs111768745

NCBI 1000 Genomes Browser:

rs111768745

Molecular consequence:

NM_001160372.4:c.3149G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001321646.2:c.3122G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001374682.1:c.3170G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001374683.1:c.3038G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001374684.1:c.3005G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_031466.8:c.3149G>A - missense variant - [Sequence Ontology: SO:0001583]
NR_164662.1:n.3311G>A - non-coding transcript variant - [Sequence Ontology: SO:0001619]

Observations:

Condition(s)

Synonyms:: none provided; RECLASSIFIED - ADRA2C POLYMORPHISM; RECLASSIFIED - ADRB1 POLYMORPHISM
Identifiers:: MedGen: C3661900

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV002063213	CeGaT Center for Human Genetics Tuebingen	criteria provided, single submitter (CeGaT Center For Human Genetics Tuebingen Variant Classification Criteria Version 2)	Likely benign (Oct 1, 2021)	germline	clinical testing	Citation Link,
SCV002341526	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Likely benign (Jan 21, 2024)	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

SCV002063213

CeGaT Center for Human Genetics Tuebingen

criteria provided, single submitter

(CeGaT Center For Human Genetics Tuebingen Variant Classification Criteria Version 2)

Likely benign
(Oct 1, 2021)

germline

clinical testing

Citation Link,

SCV002341526

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Likely benign
(Jan 21, 2024)

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
not provided	germline	yes	1	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 CeGaT Center for Human Genetics Tuebingen, SCV002063213.21

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

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

From Labcorp Genetics (formerly Invitae), Labcorp, SCV002341526.3

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

#	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: Dec 22, 2024

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