NM_030962.4(SBF2):c.3290C>A (p.Thr1097Asn) AND not provided

Germline classification:: Conflicting classifications of pathogenicity (4 submissions)
Last evaluated:: Dec 1, 2024
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:: RCV000416078.42

Allele description [Variation Report for NM_030962.4(SBF2):c.3290C>A (p.Thr1097Asn)]

NM_030962.4(SBF2):c.3290C>A (p.Thr1097Asn)

Genes:

SBF2:SET binding factor 2 [Gene - OMIM - HGNC]
LOC101928008:uncharacterized LOC101928008 [Gene]

Variant type:

single nucleotide variant

Cytogenetic location:

11p15.4

Genomic location:

Preferred name:

NM_030962.4(SBF2):c.3290C>A (p.Thr1097Asn)

HGVS:

NC_000011.10:g.9839663G>T
NG_008074.1:g.459545C>A
NM_001386339.1:c.3290C>A
NM_001386342.1:c.3161C>A
NM_030962.4:c.3290C>AMANE SELECT
NP_001373268.1:p.Thr1097Asn
NP_001373271.1:p.Thr1054Asn
NP_112224.1:p.Thr1097Asn
NP_112224.1:p.Thr1097Asn
LRG_267t1:c.3290C>A
LRG_267:g.459545C>A
LRG_267p1:p.Thr1097Asn
NC_000011.9:g.9861210G>T
NM_030962.3:c.3290C>A
p.Thr1097Asn

Protein change:

T1054N

Links:

dbSNP: rs141894081

NCBI 1000 Genomes Browser:

rs141894081

Molecular consequence:

NM_001386339.1:c.3290C>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001386342.1:c.3161C>A - missense variant - [Sequence Ontology: SO:0001583]
NM_030962.4:c.3290C>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
SCV000293367	GeneDx	criteria provided, single submitter (GeneDx Variant Classification Process June 2021)	Likely benign (Oct 30, 2020)	germline	clinical testing	Citation Link,
SCV000493523	CeGaT Center for Human Genetics Tuebingen	criteria provided, single submitter (CeGaT Center For Human Genetics Tuebingen Variant Classification Criteria Version 2)	Likely benign (Dec 1, 2024)	germline	clinical testing	Citation Link,
SCV001475456	Athena Diagnostics	criteria provided, single submitter (Athena Diagnostics Criteria)	Uncertain significance (Mar 28, 2023)	unknown	clinical testing	PubMed (6) [See all records that cite these PMIDs] 32376792, 29590070, 22730194, 28440294, 32906206, 26467025
SCV001716092	Mayo Clinic Laboratories, Mayo Clinic	criteria provided, single submitter (ACMG Guidelines, 2015)	Uncertain significance (Jun 9, 2019)	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	yes	2	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	unknown	unknown	not provided	not provided	not provided	not provided	not provided	clinical testing

Citations

PubMed

Comprehensive genetic sequence and copy number analysis for Charcot-Marie-Tooth disease in a Canadian cohort of 2517 patients.

Volodarsky M, Kerkhof J, Stuart A, Levy M, Brady LI, Tarnopolsky M, Lin H, Ainsworth P, Sadikovic B.

J Med Genet. 2021 Apr;58(4):284-288. doi: 10.1136/jmedgenet-2019-106641. Epub 2020 May 6.

PubMed [citation]

PMID:: 32376792

Phenotype risk scores identify patients with unrecognized Mendelian disease patterns.

Bastarache L, Hughey JJ, Hebbring S, Marlo J, Zhao W, Ho WT, Van Driest SL, McGregor TL, Mosley JD, Wells QS, Temple M, Ramirez AH, Carroll R, Osterman T, Edwards T, Ruderfer D, Velez Edwards DR, Hamid R, Cogan J, Glazer A, Wei WQ, Feng Q, et al.

Science. 2018 Mar 16;359(6381):1233-1239. doi: 10.1126/science.aal4043.

PubMed [citation]

PMID:: 29590070
PMCID:: PMC5959723

See all PubMed Citations (7)

Details of each submission

From GeneDx, SCV000293367.9

#	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: 32376792)

#	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, SCV000493523.37

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

Description

SBF2: BP1

#	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		2	not provided	not provided	not provided

From Athena Diagnostics, SCV001475456.2

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (6)

Description

Available data are insufficient to determine the clinical significance of the variant at this time. The frequency of this variant in the general population is higher than would generally be expected for pathogenic variants in this gene (http://gnomad.broadinstitute.org). Computational tools disagree on the variant's effect on normal protein function.

#	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

From Mayo Clinic Laboratories, Mayo Clinic, SCV001716092.1

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

Last Updated: May 25, 2025

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