NM_002382.5(MAX):c.348del (p.Ser117fs) AND Hereditary cancer-predisposing syndrome

Germline classification:: Likely pathogenic (1 submission)
Last evaluated:: Feb 28, 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:: RCV003188031.2

Allele description [Variation Report for NM_002382.5(MAX):c.348del (p.Ser117fs)]

NM_002382.5(MAX):c.348del (p.Ser117fs)

Gene:

MAX:MYC associated factor X [Gene - OMIM - HGNC]

Variant type:

Deletion

Cytogenetic location:

14q23.3

Genomic location:

Preferred name:

NM_002382.5(MAX):c.348del (p.Ser117fs)

HGVS:

NC_000014.9:g.65076614del
NG_029830.1:g.30899del
NM_001271069.2:c.144+17097del
NM_001320415.2:c.159del
NM_001407094.1:c.348del
NM_001407095.1:c.321del
NM_001407096.1:c.*121del
NM_001407097.1:c.*137del
NM_001407098.1:c.240del
NM_001407099.1:c.*121del
NM_001407100.1:c.*137del
NM_001407101.1:c.*137del
NM_001407102.1:c.*121del
NM_001407103.1:c.*137del
NM_001407104.1:c.*121del
NM_001407105.1:c.159del
NM_001407106.1:c.159del
NM_001407107.1:c.159del
NM_001407108.1:c.*121del
NM_001407109.1:c.*137del
NM_001407110.1:c.*137del
NM_001407111.1:c.147del
NM_001407112.1:c.147del
NM_002382.5:c.348delMANE SELECT
NM_145112.3:c.321del
NM_145113.3:c.*137del
NM_197957.4:c.171+17097del
NP_001307344.1:p.Ser54fs
NP_001394023.1:p.Ser117fs
NP_001394024.1:p.Ser108fs
NP_001394027.1:p.Ser81fs
NP_001394034.1:p.Ser54fs
NP_001394035.1:p.Ser54fs
NP_001394036.1:p.Ser54fs
NP_001394040.1:p.Ser50fs
NP_001394041.1:p.Ser50fs
NP_002373.3:p.Ser117Profs
NP_002373.3:p.Ser117fs
NP_660087.1:p.Ser108fs
LRG_530t1:c.345del
LRG_530:g.30899del
LRG_530p1:p.Ser117Profs
NC_000014.8:g.65543332del
NM_002382.3:c.345delC
NM_002382.3:c.348delC
NR_073137.2:n.472del
NR_176275.1:n.591del
NR_176278.1:n.321del
NR_176279.1:n.525del
NR_176280.1:n.490del
NR_176281.1:n.672del
NR_176282.1:n.395del

Protein change:

S108fs

Molecular consequence:

NM_001407096.1:c.*121del - 3 prime UTR variant - [Sequence Ontology: SO:0001624]
NM_001407097.1:c.*137del - 3 prime UTR variant - [Sequence Ontology: SO:0001624]
NM_001407099.1:c.*121del - 3 prime UTR variant - [Sequence Ontology: SO:0001624]
NM_001407100.1:c.*137del - 3 prime UTR variant - [Sequence Ontology: SO:0001624]
NM_001407101.1:c.*137del - 3 prime UTR variant - [Sequence Ontology: SO:0001624]
NM_001407102.1:c.*121del - 3 prime UTR variant - [Sequence Ontology: SO:0001624]
NM_001407103.1:c.*137del - 3 prime UTR variant - [Sequence Ontology: SO:0001624]
NM_001407104.1:c.*121del - 3 prime UTR variant - [Sequence Ontology: SO:0001624]
NM_001407108.1:c.*121del - 3 prime UTR variant - [Sequence Ontology: SO:0001624]
NM_001407109.1:c.*137del - 3 prime UTR variant - [Sequence Ontology: SO:0001624]
NM_001407110.1:c.*137del - 3 prime UTR variant - [Sequence Ontology: SO:0001624]
NM_145113.3:c.*137del - 3 prime UTR variant - [Sequence Ontology: SO:0001624]
NM_001320415.2:c.159del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001407094.1:c.348del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001407095.1:c.321del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001407098.1:c.240del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001407105.1:c.159del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001407106.1:c.159del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001407107.1:c.159del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001407111.1:c.147del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001407112.1:c.147del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_002382.5:c.348del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_145112.3:c.321del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001271069.2:c.144+17097del - intron variant - [Sequence Ontology: SO:0001627]
NM_197957.4:c.171+17097del - intron variant - [Sequence Ontology: SO:0001627]
NR_073137.2:n.472del - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_176275.1:n.591del - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_176278.1:n.321del - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_176279.1:n.525del - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_176280.1:n.490del - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_176281.1:n.672del - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_176282.1:n.395del - non-coding transcript variant - [Sequence Ontology: SO:0001619]

Condition(s)

Name:: Hereditary cancer-predisposing syndrome
Synonyms:: Neoplastic Syndromes, Hereditary; Tumor predisposition; Cancer predisposition; See all synonyms [MedGen]
Identifiers:: MONDO: MONDO:0015356; MeSH: D009386; MedGen: C0027672

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV003866457	Ambry Genetics	criteria provided, single submitter (Ambry Variant Classification Scheme 2023)	Likely pathogenic (Feb 28, 2023)	germline	clinical testing	Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV003866457

Ambry Genetics

criteria provided, single submitter

(Ambry Variant Classification Scheme 2023)

Likely pathogenic
(Feb 28, 2023)

germline

clinical testing

Citation Link

Help

Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	germline	unknown	not provided	not provided	not provided	not provided	not provided	clinical testing

Details of each submission

From Ambry Genetics, SCV003866457.2

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

Description

The c.348delC variant, located in coding exon 5 of the MAX gene, results from a deletion of one nucleotide at nucleotide position 348, causing a translational frameshift with a predicted alternate stop codon (p.S117Pfs*53). This alteration occurs at the 3' terminus of theMAX gene, is not expected to trigger nonsense-mediated mRNAdecay and results in the elongation of the protein by 8 amino acids. This frameshift impacts the last 45amino acids of the native protein. However, frameshifts are typically deleterious in nature and a significant portion of the protein is affected (Ambry internal data). This variant is considered to be rare based on population cohorts in the Genome Aggregation Database (gnomAD). Based on the majority of available evidence to date, this variant is likely to be pathogenic.

#	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		not provided	not provided	not provided	not provided

Last Updated: May 1, 2024

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