NM_003200.5(TCF3):c.1049C>T (p.Ser350Leu) AND Agammaglobulinemia 8, autosomal dominant

Germline classification:: Uncertain significance (1 submission)
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:: RCV001823580.3

Allele description [Variation Report for NM_003200.5(TCF3):c.1049C>T (p.Ser350Leu)]

NM_003200.5(TCF3):c.1049C>T (p.Ser350Leu)

Gene:

TCF3:transcription factor 3 [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

19p13.3

Genomic location:

Preferred name:

NM_003200.5(TCF3):c.1049C>T (p.Ser350Leu)

HGVS:

NC_000019.10:g.1621012G>A
NG_029953.2:g.36535C>T
NM_001136139.4:c.1049C>T
NM_001351778.2:c.1049C>T
NM_001351779.2:c.1049C>T
NM_003200.5:c.1049C>TMANE SELECT
NP_001129611.1:p.Ser350Leu
NP_001338707.1:p.Ser350Leu
NP_001338708.1:p.Ser350Leu
NP_003191.1:p.Ser350Leu
LRG_1325t1:c.1049C>T
LRG_1325t2:c.1049C>T
LRG_1325:g.36535C>T
LRG_1325p1:p.Ser350Leu
LRG_1325p2:p.Ser350Leu
NC_000019.9:g.1621011G>A
NM_003200.5:c.[1049C>T]MANE SELECT

Protein change:

S350L

Links:

dbSNP: rs963433488

NCBI 1000 Genomes Browser:

rs963433488

Molecular consequence:

NM_001136139.4:c.1049C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001351778.2:c.1049C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001351779.2:c.1049C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_003200.5:c.1049C>T - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Name:: Agammaglobulinemia 8, autosomal dominant (AGM8A)
Synonyms:: AGAMMAGLOBULINEMIA, AUTOSOMAL DOMINANT, DUE TO TCF3 DEFECT; AGAMMAGLOBULINEMIA 8A, AUTOSOMAL DOMINANT
Identifiers:: MONDO: MONDO:0014840; MedGen: C4310786; OMIM: 616941

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV002073129	Neuberg Centre For Genomic Medicine, NCGM	criteria provided, single submitter (ACMG Guidelines, 2015)	Uncertain significance	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

SCV002073129

Neuberg Centre For Genomic Medicine, NCGM

criteria provided, single submitter

(ACMG Guidelines, 2015)

Uncertain significance

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	not provided	not provided	not provided	not provided	not provided	clinical testing

Citations

PubMed

Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology.

Richards S, Aziz N, Bale S, Bick D, Das S, Gastier-Foster J, Grody WW, Hegde M, Lyon E, Spector E, Voelkerding K, Rehm HL; ACMG Laboratory Quality Assurance Committee..

Genet Med. 2015 May;17(5):405-24. doi: 10.1038/gim.2015.30. Epub 2015 Mar 5.

PubMed [citation]

PMID:: 25741868
PMCID:: PMC4544753

Details of each submission

From Neuberg Centre For Genomic Medicine, NCGM, SCV002073129.1

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

Description

The missense variant p.S350L in TCF3 (NM_003200.5) has not been reported previously as a pathogenic variant nor as a benign variant, to our knowledge. The p.S350L variant is novel (not in any individuals) in 1000 Genomes and novel (not in any individuals) in gnomAD Exomes. The p.S350L missense variant is predicted to be damaging by both SIFT and PolyPhen2. The nucleotide c.1049 in TCF3 is predicted conserved by GERP++ and PhyloP across 100 vertebrates. For these reasons, this variant has been classified as Uncertain Significance.

#	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

Last Updated: Apr 6, 2024

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