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NM_016734.3(PAX5):c.638C>T (p.Ser213Leu) AND Leukemia, acute lymphoblastic, susceptibility to, 3

Germline classification:
Likely benign (1 submission)
Last evaluated:
Feb 11, 2021
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:
RCV001554278.3

Allele description [Variation Report for NM_016734.3(PAX5):c.638C>T (p.Ser213Leu)]

NM_016734.3(PAX5):c.638C>T (p.Ser213Leu)

Gene:
PAX5:paired box 5 [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
9p13.2
Genomic location:
Preferred name:
NM_016734.3(PAX5):c.638C>T (p.Ser213Leu)
HGVS:
  • NC_000009.12:g.36966691G>A
  • NG_033894.1:g.72789C>T
  • NM_001280547.2:c.638C>T
  • NM_001280548.2:c.638C>T
  • NM_001280549.2:c.638C>T
  • NM_001280550.2:c.638C>T
  • NM_001280551.2:c.314C>T
  • NM_001280552.2:c.638C>T
  • NM_001280553.2:c.509C>T
  • NM_001280554.2:c.509C>T
  • NM_001280555.2:c.440C>T
  • NM_001280556.2:c.314C>T
  • NM_016734.3:c.638C>TMANE SELECT
  • NP_001267476.1:p.Ser213Leu
  • NP_001267477.1:p.Ser213Leu
  • NP_001267478.1:p.Ser213Leu
  • NP_001267479.1:p.Ser213Leu
  • NP_001267480.1:p.Ser105Leu
  • NP_001267481.1:p.Ser213Leu
  • NP_001267482.1:p.Ser170Leu
  • NP_001267483.1:p.Ser170Leu
  • NP_001267484.1:p.Ser147Leu
  • NP_001267485.1:p.Ser105Leu
  • NP_057953.1:p.Ser213Leu
  • LRG_1384t1:c.638C>T
  • LRG_1384:g.72789C>T
  • LRG_1384p1:p.Ser213Leu
  • NC_000009.11:g.36966688G>A
  • NM_016734.2:c.638C>T
  • NR_103999.2:n.875C>T
  • NR_104000.2:n.875C>T
  • Q02548:p.Ser213Leu
Protein change:
S105L
Links:
UniProtKB: Q02548#VAR_070684; dbSNP: rs137870876
NCBI 1000 Genomes Browser:
rs137870876
Molecular consequence:
  • NM_001280547.2:c.638C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001280548.2:c.638C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001280549.2:c.638C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001280550.2:c.638C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001280551.2:c.314C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001280552.2:c.638C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001280553.2:c.509C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001280554.2:c.509C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001280555.2:c.440C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001280556.2:c.314C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_016734.3:c.638C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NR_103999.2:n.875C>T - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NR_104000.2:n.875C>T - non-coding transcript variant - [Sequence Ontology: SO:0001619]

Condition(s)

Name:
Leukemia, acute lymphoblastic, susceptibility to, 3 (ALL3)
Identifiers:
MONDO: MONDO:0014241; MedGen: C3809874; OMIM: 615545

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Assertion and evidence details

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Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV001775504St. Jude Molecular Pathology, St. Jude Children's Research Hospital
criteria provided, single submitter

(St. Jude Assertion Criteria 2020)		Likely benign
(Feb 11, 2021) 		germlineclinical testing

Citation Link

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Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineunknownnot providednot providednot providednot providednot providedclinical testing

Details of each submission

From St. Jude Molecular Pathology, St. Jude Children's Research Hospital, SCV001775504.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testingnot provided

Description

The PAX5 c.638C>T (p.Ser213Leu) missense change has a maximum subpopulation frequency of 0.11% in gnomAD v2.1.1 (https://gnomad.broadinstitute.org/variant/9-36966688-G-A?dataset=gnomad_r2_1). This population frequency is higher than expected for a pathogenic variant in PAX5 causing predisposition to acute lymphoblastic leukemia (BS1). In silico tools are not in agreement about the effect on the gene or protein function and functional studies have not been performed. This variant has been identified in patients without a personal or family history of acute lymphoblastic leukemia (internal data). In summary, this variant meets criteria to be classified as likely benign based on the ACMG/AMP criteria: BS1.

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknownnot providednot providednot providednot providednot providednot providednot provided

Last Updated: Sep 29, 2024