NM_004304.5(ALK):c.3524A>G (p.Asn1175Ser) AND Hereditary cancer-predisposing syndrome

Germline classification:: Uncertain significance (2 submissions)
Last evaluated:: Nov 10, 2022
Review status:: 2 stars out of maximum of 4 stars
criteria provided, multiple submitters, no conflicts

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:: RCV002257826.5

Allele description [Variation Report for NM_004304.5(ALK):c.3524A>G (p.Asn1175Ser)]

NM_004304.5(ALK):c.3524A>G (p.Asn1175Ser)

Gene:

ALK:ALK receptor tyrosine kinase [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

2p23.2

Genomic location:

Preferred name:

NM_004304.5(ALK):c.3524A>G (p.Asn1175Ser)

HGVS:

NC_000002.12:g.29220827T>C
NG_009445.1:g.705740A>G
NM_001353765.2:c.320A>G
NM_004304.5:c.3524A>GMANE SELECT
NP_001340694.1:p.Asn107Ser
NP_004295.2:p.Asn1175Ser
LRG_488t1:c.3524A>G
LRG_488:g.705740A>G
NC_000002.11:g.29443693T>C
NM_004304.3:c.3524A>G
NM_004304.4:c.3524A>G

Protein change:

N107S

Links:

dbSNP: rs774872969

NCBI 1000 Genomes Browser:

rs774872969

Molecular consequence:

NM_001353765.2:c.320A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_004304.5:c.3524A>G - missense variant - [Sequence Ontology: SO:0001583]

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

Recent activity

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histone-lysine N-methyltransferase SETDB1 isoform X3 [Homo sapiens]
histone-lysine N-methyltransferase SETDB1 isoform X3 [Homo sapiens]
gi|2462515956|ref|XP_054195854.1|

Protein
PKP4-AS1 PKP4 antisense RNA 1 [Homo sapiens]
PKP4-AS1 PKP4 antisense RNA 1 [Homo sapiens]
Gene ID:100129029

Gene
100129029[uid] AND (alive[prop]) (1)
Gene
Avian paramyxovirus 1 isolate A373, complete genome
Avian paramyxovirus 1 isolate A373, complete genome
gi|1974981334|gb|MW342779.1|

Nucleotide
Coprinellus sp. voucher K:140930 18S ribosomal RNA gene, partial sequence; inter...
Coprinellus sp. voucher K:140930 18S ribosomal RNA gene, partial sequence; internal transcribed spacer 1, 5.8S ribosomal RNA gene, and internal transcribed spacer 2, complete sequence; and 28S ribosomal RNA gene, partial sequence
gi|1653974345|gb|MK077827.1|

Nucleotide

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV002528481	Sema4, Sema4	criteria provided, single submitter (Sema4 Curation Guidelines)	Uncertain significance (Nov 25, 2021)	germline	curation	Citation Link,
SCV002613415	Ambry Genetics	criteria provided, single submitter (Ambry Variant Classification Scheme 2023)	Uncertain significance (Nov 10, 2022)	germline	clinical testing	Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV002528481

Sema4, Sema4

criteria provided, single submitter

(Sema4 Curation Guidelines)

Uncertain significance
(Nov 25, 2021)

germline

curation

Citation Link,

SCV002613415

Ambry Genetics

criteria provided, single submitter

(Ambry Variant Classification Scheme 2023)

Uncertain significance
(Nov 10, 2022)

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, curation

Details of each submission

From Sema4, Sema4, SCV002528481.1

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

#	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

From Ambry Genetics, SCV002613415.3

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

Description

The p.N1175S variant (also known as c.3524A>G), located in coding exon 23 of the ALK gene, results from an A to G substitution at nucleotide position 3524. The asparagine at codon 1175 is replaced by serine, an amino acid with highly similar properties. This amino acid position is well conserved in available vertebrate species. In addition, this alteration is predicted to be tolerated by in silico analysis. Since supporting evidence is limited at this time, the clinical significance of this alteration remains unclear.

#	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: Sep 29, 2024

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