NM_030962.4(SBF2):c.5014_5016del (p.Lys1672del) AND not provided

Germline classification:: Uncertain significance (3 submissions)
Last evaluated:: May 18, 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:: RCV000513369.31

Allele description [Variation Report for NM_030962.4(SBF2):c.5014_5016del (p.Lys1672del)]

NM_030962.4(SBF2):c.5014_5016del (p.Lys1672del)

Genes:

SBF2-AS1:SBF2 antisense RNA 1 [Gene - HGNC]
SBF2:SET binding factor 2 [Gene - OMIM - HGNC]
LOC105369149:uncharacterized LOC105369149 [Gene]

Variant type:

Deletion

Cytogenetic location:

11p15.4

Genomic location:

Preferred name:

NM_030962.4(SBF2):c.5014_5016del (p.Lys1672del)

HGVS:

NC_000011.10:g.9787655_9787657del
NG_008074.1:g.511551_511553del
NM_001386339.1:c.5110_5112del
NM_001386342.1:c.4885_4887del
NM_030962.4:c.5014_5016delMANE SELECT
NP_001373268.1:p.Lys1704del
NP_001373271.1:p.Lys1629del
NP_112224.1:p.Lys1672del
LRG_267:g.511551_511553del
NC_000011.9:g.9809202_9809204del
NM_030962.3:c.5014_5016delAAA

Protein change:

K1629del

Links:

dbSNP: rs750958357

NCBI 1000 Genomes Browser:

rs750958357

Molecular consequence:

NM_001386339.1:c.5110_5112del - inframe_deletion - [Sequence Ontology: SO:0001822]
NM_001386342.1:c.4885_4887del - inframe_deletion - [Sequence Ontology: SO:0001822]
NM_030962.4:c.5014_5016del - inframe_deletion - [Sequence Ontology: SO:0001822]

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
SCV000589401	GeneDx	criteria provided, single submitter (GeneDx Variant Classification Process June 2021)	Uncertain significance (May 18, 2024)	germline	clinical testing	Citation Link,
SCV000608579	CeGaT Center for Human Genetics Tuebingen	criteria provided, single submitter (CeGaT Center For Human Genetics Tuebingen Variant Classification Criteria Version 2)	Uncertain significance (Jun 1, 2017)	germline	clinical testing	Citation Link,
SCV000615015	Athena Diagnostics	criteria provided, single submitter (Athena Diagnostics Criteria)	Uncertain significance (Aug 4, 2022)	unknown	clinical testing	PubMed (3) [See all records that cite these PMIDs] 27582484, 26392352, 26467025

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000589401

GeneDx

criteria provided, single submitter

(GeneDx Variant Classification Process June 2021)

Uncertain significance
(May 18, 2024)

germline

clinical testing

Citation Link,

SCV000608579

CeGaT Center for Human Genetics Tuebingen

criteria provided, single submitter

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

Uncertain significance
(Jun 1, 2017)

germline

clinical testing

Citation Link,

SCV000615015

Athena Diagnostics

criteria provided, single submitter

(Athena Diagnostics Criteria)

Uncertain significance
(Aug 4, 2022)

unknown

clinical testing

PubMed (3)
[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	yes	1	not provided	not provided	not provided	not provided	clinical testing
not provided	unknown	unknown	not provided	not provided	not provided	not provided	not provided	clinical testing

Citations

PubMed

Targeted Sequencing Reveals Low-Frequency Variants in EPHA Genes as Markers of Paclitaxel-Induced Peripheral Neuropathy.

Apellániz-Ruiz M, Tejero H, Inglada-Pérez L, Sánchez-Barroso L, Gutiérrez-Gutiérrez G, Calvo I, Castelo B, Redondo A, García-Donás J, Romero-Laorden N, Sereno M, Merino M, Currás-Freixes M, Montero-Conde C, Mancikova V, Åvall-Lundqvist E, Green H, Al-Shahrour F, Cascón A, Robledo M, Rodríguez-Antona C.

Clin Cancer Res. 2017 Mar 1;23(5):1227-1235. doi: 10.1158/1078-0432.CCR-16-0694. Epub 2016 Aug 31.

PubMed [citation]

PMID:: 27582484

Application of targeted multi-gene panel testing for the diagnosis of inherited peripheral neuropathy provides a high diagnostic yield with unexpected phenotype-genotype variability.

Antoniadi T, Buxton C, Dennis G, Forrester N, Smith D, Lunt P, Burton-Jones S.

BMC Med Genet. 2015 Sep 21;16:84. doi: 10.1186/s12881-015-0224-8.

PubMed [citation]

PMID:: 26392352
PMCID:: PMC4578331

See all PubMed Citations (3)

Details of each submission

From GeneDx, SCV000589401.6

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

Description

Identified along with a second SBF2 variant in a patient with spastic paraplegia and leukodystrophy, but segregation information was not provided (PMID: 30212743); Observed in apparent homozygous state in a patient with suspected Charcot-Marie-Tooth disease in the literature who also had a variant in another gene that may have been responsible for the phenotype (PMID: 36790232); In silico analysis supports a deleterious effect on protein structure/function; In-frame deletion of 1 amino acids in a non-repeat region; This variant is associated with the following publications: (PMID: 27582484, 26392352, 30212743, 36790232)

#	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 CeGaT Center for Human Genetics Tuebingen, SCV000608579.30

#	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 Athena Diagnostics, SCV000615015.2

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (3)

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

Last Updated: Oct 8, 2024

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