NM_152564.5(VPS13B):c.1768G>A (p.Ala590Thr) AND not provided

Germline classification:: Conflicting interpretations of pathogenicity (7 submissions)
Last evaluated:: Jan 1, 2023
Review status:: criteria provided, conflicting classifications

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:: RCV000711291.33

Allele description [Variation Report for NM_152564.5(VPS13B):c.1768G>A (p.Ala590Thr)]

NM_152564.5(VPS13B):c.1768G>A (p.Ala590Thr)

Gene:

VPS13B:vacuolar protein sorting 13 homolog B [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

8q22.2

Genomic location:

Preferred name:

NM_152564.5(VPS13B):c.1768G>A (p.Ala590Thr)

HGVS:

NC_000008.11:g.99143090G>A
NG_007098.2:g.134825G>A
NM_015243.3:c.1768G>A
NM_017890.5:c.1768G>A
NM_152564.5:c.1768G>AMANE SELECT
NP_056058.2:p.Ala590Thr
NP_060360.3:p.Ala590Thr
NP_060360.3:p.Ala590Thr
NP_689777.3:p.Ala590Thr
LRG_351t1:c.1768G>A
LRG_351t2:c.1768G>A
LRG_351:g.134825G>A
LRG_351p1:p.Ala590Thr
NC_000008.10:g.100155318G>A
NM_017890.3:c.1768G>A
NM_017890.4:c.1768G>A
NM_152564.4:c.1768G>A

Protein change:

A590T

Links:

dbSNP: rs140601319

NCBI 1000 Genomes Browser:

rs140601319

Molecular consequence:

NM_015243.3:c.1768G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_017890.5:c.1768G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_152564.5:c.1768G>A - missense variant - [Sequence Ontology: SO:0001583]

Observations:

Condition(s)

Synonyms:: none provided
Identifiers:: MedGen: C3661900

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000225902	Eurofins Ntd Llc (ga)	criteria provided, single submitter (EGL Classification Definitions 2015)	Uncertain significance (Oct 17, 2014)	germline	clinical testing	Citation Link,
SCV000564894	GeneDx	criteria provided, single submitter (GeneDx Variant Classification Process June 2021)	Likely benign (Dec 16, 2020)	germline	clinical testing	Citation Link,
SCV000841628	Athena Diagnostics Inc	criteria provided, single submitter (Athena Diagnostics Criteria)	Uncertain significance (Sep 27, 2017)	germline	clinical testing	PubMed (2) [See all records that cite these PMIDs] 17990063, 26467025
SCV001746048	CeGaT Center for Human Genetics Tuebingen	criteria provided, single submitter (CeGaT Center For Human Genetics Tuebingen Variant Classification Criteria Version 2)	Likely benign (Jan 1, 2023)	germline	clinical testing	Citation Link,
SCV001979228	Clinical Genetics, Academic Medical Center - VKGL Data-share Consensus See additional submitters Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen	no assertion criteria provided	Likely benign	germline	clinical testing
SCV001980048	Clinical Genetics DNA and cytogenetics Diagnostics Lab, Erasmus MC, Erasmus Medical Center - VKGL Data-share Consensus See additional submitters Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen	no assertion criteria provided	Likely benign	germline	clinical testing
SCV004025956	Institute for Clinical Genetics, University Hospital TU Dresden, University Hospital TU Dresden	criteria provided, single submitter (ACMG Guidelines, 2015)	Uncertain significance (Sep 28, 2020)	maternal	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	yes	4	not provided	not provided	not provided	not provided	clinical testing
not provided	germline	unknown	1	not provided	not provided	not provided	not provided	clinical testing
not provided	maternal	not provided	not provided	not provided	not provided	not provided	not provided	clinical testing

Citations

PubMed

Clinical and molecular characterization of Italian patients affected by Cohen syndrome.

Katzaki E, Pescucci C, Uliana V, Papa FT, Ariani F, Meloni I, Priolo M, Selicorni A, Milani D, Fischetto R, Celle ME, Grasso R, Dallapiccola B, Brancati F, Bordignon M, Tenconi R, Federico A, Mari F, Renieri A, Longo I.

J Hum Genet. 2007;52(12):1011-1017. doi: 10.1007/s10038-007-0208-4. Epub 2007 Nov 8. Erratum in: J Hum Genet. 2008 Mar;53(3):285. J Hum Genet. 2008 Mar;53(3):285.

PubMed [citation]

PMID:: 17990063

A Standardized DNA Variant Scoring System for Pathogenicity Assessments in Mendelian Disorders.

Karbassi I, Maston GA, Love A, DiVincenzo C, Braastad CD, Elzinga CD, Bright AR, Previte D, Zhang K, Rowland CM, McCarthy M, Lapierre JL, Dubois F, Medeiros KA, Batish SD, Jones J, Liaquat K, Hoffman CA, Jaremko M, Wang Z, Sun W, Buller-Burckle A, et al.

Hum Mutat. 2016 Jan;37(1):127-34. doi: 10.1002/humu.22918. Epub 2015 Oct 29.

PubMed [citation]

PMID:: 26467025
PMCID:: PMC4737317

See all PubMed Citations (3)

Details of each submission

From Eurofins Ntd Llc (ga), SCV000225902.5

#	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	unknown	not provided	not provided	not provided		1	not provided	not provided	not provided

From GeneDx, SCV000564894.4

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

Description

This variant is associated with the following publications: (PMID: 17990063, 19006247)

#	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		not provided	not provided	not provided	not provided

From Athena Diagnostics Inc, SCV000841628.1

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

#	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

From CeGaT Center for Human Genetics Tuebingen, SCV001746048.14

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	4	not provided	not provided	clinical testing	not provided

Description

VPS13B: BP4, BP5, BS2

#	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		4	not provided	not provided	not provided

From Clinical Genetics, Academic Medical Center - VKGL Data-share Consensus, SCV001979228.1

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

From Clinical Genetics DNA and cytogenetics Diagnostics Lab, Erasmus MC, Erasmus Medical Center - VKGL Data-share Consensus, SCV001980048.1

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

From Institute for Clinical Genetics, University Hospital TU Dresden, University Hospital TU Dresden, SCV004025956.1

#	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	maternal	not provided	not provided	not provided	not provided		not provided	not provided	not provided	not provided

Last Updated: Apr 20, 2024

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