NM_018921.3(PCDHGA9):c.1537G>A (p.Val513Met) AND not specified

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Nov 27, 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:: RCV004500435.1

Allele description [Variation Report for NM_018921.3(PCDHGA9):c.1537G>A (p.Val513Met)]

NM_018921.3(PCDHGA9):c.1537G>A (p.Val513Met)

Genes:

PCDHG@:protocadherin gamma cluster [Gene - OMIM - HGNC]
PCDHGA1:protocadherin gamma subfamily A, 1 [Gene - OMIM - HGNC]
PCDHGA2:protocadherin gamma subfamily A, 2 [Gene - OMIM - HGNC]
PCDHGA3:protocadherin gamma subfamily A, 3 [Gene - OMIM - HGNC]
PCDHGA4:protocadherin gamma subfamily A, 4 [Gene - OMIM - HGNC]
PCDHGA5:protocadherin gamma subfamily A, 5 [Gene - OMIM - HGNC]
PCDHGA6:protocadherin gamma subfamily A, 6 [Gene - OMIM - HGNC]
PCDHGA7:protocadherin gamma subfamily A, 7 [Gene - OMIM - HGNC]
PCDHGA8:protocadherin gamma subfamily A, 8 [Gene - OMIM - HGNC]
PCDHGA9:protocadherin gamma subfamily A, 9 [Gene - OMIM - HGNC]
PCDHGB1:protocadherin gamma subfamily B, 1 [Gene - OMIM - HGNC]
PCDHGB2:protocadherin gamma subfamily B, 2 [Gene - OMIM - HGNC]
PCDHGB3:protocadherin gamma subfamily B, 3 [Gene - OMIM - HGNC]
PCDHGB4:protocadherin gamma subfamily B, 4 [Gene - OMIM - HGNC]
PCDHGB5:protocadherin gamma subfamily B, 5 [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

5q31.3

Genomic location:

Preferred name:

NM_018921.3(PCDHGA9):c.1537G>A (p.Val513Met)

HGVS:

NC_000005.10:g.141404489G>A
NG_000012.2:g.114686G>A
NM_003736.4:c.2397+14208G>AMANE SELECT
NM_018912.3:c.2421+71384G>AMANE SELECT
NM_018915.4:c.2424+63094G>AMANE SELECT
NM_018916.4:c.2424+58032G>AMANE SELECT
NM_018917.4:c.2514+46868G>AMANE SELECT
NM_018918.3:c.2421+37738G>AMANE SELECT
NM_018919.3:c.2424+27982G>AMANE SELECT
NM_018920.4:c.2424+19166G>AMANE SELECT
NM_018921.3:c.1537G>AMANE SELECT
NM_018922.3:c.2409+51820G>AMANE SELECT
NM_018923.3:c.2421+41933G>AMANE SELECT
NM_018924.5:c.2415+31680G>AMANE SELECT
NM_018925.3:c.2397+3965G>AMANE SELECT
NM_032088.2:c.2424+9252G>AMANE SELECT
NM_032089.2:c.1537G>A
NP_061744.1:p.Val513Met
NP_114478.1:p.Val513Met
NC_000005.9:g.140784056G>A
NM_018921.2:c.1537G>A

Protein change:

V513M

Molecular consequence:

NM_003736.4:c.2397+14208G>A - intron variant - [Sequence Ontology: SO:0001627]
NM_018912.3:c.2421+71384G>A - intron variant - [Sequence Ontology: SO:0001627]
NM_018915.4:c.2424+63094G>A - intron variant - [Sequence Ontology: SO:0001627]
NM_018916.4:c.2424+58032G>A - intron variant - [Sequence Ontology: SO:0001627]
NM_018917.4:c.2514+46868G>A - intron variant - [Sequence Ontology: SO:0001627]
NM_018918.3:c.2421+37738G>A - intron variant - [Sequence Ontology: SO:0001627]
NM_018919.3:c.2424+27982G>A - intron variant - [Sequence Ontology: SO:0001627]
NM_018920.4:c.2424+19166G>A - intron variant - [Sequence Ontology: SO:0001627]
NM_018922.3:c.2409+51820G>A - intron variant - [Sequence Ontology: SO:0001627]
NM_018923.3:c.2421+41933G>A - intron variant - [Sequence Ontology: SO:0001627]
NM_018924.5:c.2415+31680G>A - intron variant - [Sequence Ontology: SO:0001627]
NM_018925.3:c.2397+3965G>A - intron variant - [Sequence Ontology: SO:0001627]
NM_032088.2:c.2424+9252G>A - intron variant - [Sequence Ontology: SO:0001627]
NM_018921.3:c.1537G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_032089.2:c.1537G>A - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Synonyms:: AllHighlyPenetrant
Identifiers:: MedGen: CN169374

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV005001079	Ambry Genetics	criteria provided, single submitter (Ambry Variant Classification Scheme 2023)	Uncertain significance (Nov 27, 2023)	germline	clinical testing	Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV005001079

Ambry Genetics

criteria provided, single submitter

(Ambry Variant Classification Scheme 2023)

Uncertain significance
(Nov 27, 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, SCV005001079.1

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

Description

The c.1537G>A (p.V513M) alteration is located in exon 1 (coding exon 1) of the PCDHGA9 gene. This alteration results from a G to A substitution at nucleotide position 1537, causing the valine (V) at amino acid position 513 to be replaced by a methionine (M). Based on insufficient or conflicting evidence, 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 1, 2024

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