NM_016734.3(PAX5):c.134_147del (p.Ala45fs) AND Acute lymphoid leukemia

Germline classification:: Likely pathogenic (1 submission)
Last evaluated:: Sep 23, 2023
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:: RCV003444140.1

Allele description [Variation Report for NM_016734.3(PAX5):c.134_147del (p.Ala45fs)]

NM_016734.3(PAX5):c.134_147del (p.Ala45fs)

Gene:

PAX5:paired box 5 [Gene - OMIM - HGNC]

Variant type:

Deletion

Cytogenetic location:

9p13.2

Genomic location:

Preferred name:

NM_016734.3(PAX5):c.134_147del (p.Ala45fs)

HGVS:

NC_000009.12:g.37020701_37020714del
NG_033894.1:g.18766_18779del
NM_001280547.2:c.134_147del
NM_001280548.2:c.134_147del
NM_001280549.2:c.134_147del
NM_001280550.2:c.134_147del
NM_001280551.2:c.-112-5520_-112-5507del
NM_001280552.2:c.134_147del
NM_001280553.2:c.134_147del
NM_001280554.2:c.134_147del
NM_001280555.2:c.134_147del
NM_001280556.2:c.-112-5520_-112-5507del
NM_016734.3:c.134_147delMANE SELECT
NP_001267476.1:p.Ala45fs
NP_001267477.1:p.Ala45fs
NP_001267478.1:p.Ala45fs
NP_001267479.1:p.Ala45fs
NP_001267481.1:p.Ala45fs
NP_001267482.1:p.Ala45fs
NP_001267483.1:p.Ala45fs
NP_001267484.1:p.Ala45fs
NP_057953.1:p.Ala45fs
LRG_1384t1:c.134_147del
LRG_1384:g.18766_18779del
LRG_1384p1:p.Ala45fs
NC_000009.11:g.37020698_37020711del
NM_016734.2:c.134_147del
NR_103999.2:n.371_384del
NR_104000.2:n.371_384del

Protein change:

A45fs

Molecular consequence:

NM_001280547.2:c.134_147del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001280548.2:c.134_147del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001280549.2:c.134_147del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001280550.2:c.134_147del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001280552.2:c.134_147del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001280553.2:c.134_147del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001280554.2:c.134_147del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001280555.2:c.134_147del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_016734.3:c.134_147del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001280551.2:c.-112-5520_-112-5507del - intron variant - [Sequence Ontology: SO:0001627]
NM_001280556.2:c.-112-5520_-112-5507del - intron variant - [Sequence Ontology: SO:0001627]
NR_103999.2:n.371_384del - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_104000.2:n.371_384del - non-coding transcript variant - [Sequence Ontology: SO:0001619]

Condition(s)

Name:: Acute lymphoid leukemia (ALL)
Synonyms:: Acute lymphoblastic leukemia; Leukemia, acute lymphoblastic, somatic; Lymphoblastic leukemia; See all synonyms [MedGen]
Identifiers:: MONDO: MONDO:0004967; MedGen: C0023449; Orphanet: 513; OMIM: 613065; Human Phenotype Ontology: HP:0006721

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV004036069	Genomic Diagnostics Laboratory, National Institute of Medical Genomics	criteria provided, single submitter (AMP Guidelines, 2017)	Likely pathogenic (Sep 23, 2023)	somatic	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

SCV004036069

Genomic Diagnostics Laboratory, National Institute of Medical Genomics

criteria provided, single submitter

(AMP Guidelines, 2017)

Likely pathogenic
(Sep 23, 2023)

somatic

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	somatic	yes	not provided	not provided	not provided	not provided	not provided	clinical testing

Citations

PubMed

Standards and Guidelines for the Interpretation and Reporting of Sequence Variants in Cancer: A Joint Consensus Recommendation of the Association for Molecular Pathology, American Society of Clinical Oncology, and College of American Pathologists.

Li MM, Datto M, Duncavage EJ, Kulkarni S, Lindeman NI, Roy S, Tsimberidou AM, Vnencak-Jones CL, Wolff DJ, Younes A, Nikiforova MN.

J Mol Diagn. 2017 Jan;19(1):4-23. doi: 10.1016/j.jmoldx.2016.10.002. Review.

PubMed [citation]

PMID:: 27993330
PMCID:: PMC5707196

Details of each submission

From Genomic Diagnostics Laboratory, National Institute of Medical Genomics, SCV004036069.1

#	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	somatic	yes	not provided	not provided	not provided		not provided	not provided	not provided	not provided

Last Updated: Dec 2, 2023

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