NM_001384140.1(PCDH15):c.985G>A (p.Gly329Arg) AND Usher syndrome type 1F

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Jan 24, 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:: RCV002789955.2

Allele description [Variation Report for NM_001384140.1(PCDH15):c.985G>A (p.Gly329Arg)]

NM_001384140.1(PCDH15):c.985G>A (p.Gly329Arg)

Gene:

PCDH15:protocadherin related 15 [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

10q21.1

Genomic location:

Preferred name:

NM_001384140.1(PCDH15):c.985G>A (p.Gly329Arg)

Other names:

NM_001384140.1:c.985G>A

HGVS:

NC_000010.11:g.54236823C>T
NG_009191.3:g.1397360G>A
NM_001142763.2:c.1000G>A
NM_001142764.2:c.985G>A
NM_001142765.2:c.985G>A
NM_001142766.2:c.985G>A
NM_001142767.2:c.874G>A
NM_001142768.2:c.919G>A
NM_001142769.3:c.1000G>A
NM_001142770.3:c.985G>A
NM_001142771.2:c.1000G>A
NM_001142772.2:c.985G>A
NM_001142773.2:c.919G>A
NM_001354404.2:c.919G>A
NM_001354411.2:c.985G>A
NM_001354420.2:c.985G>A
NM_001354429.2:c.985G>A
NM_001354430.2:c.985G>A
NM_001384140.1:c.985G>AMANE SELECT
NM_033056.4:c.985G>A
NP_001136235.1:p.Gly334Arg
NP_001136236.1:p.Gly329Arg
NP_001136237.1:p.Gly329Arg
NP_001136238.1:p.Gly329Arg
NP_001136239.1:p.Gly292Arg
NP_001136240.1:p.Gly307Arg
NP_001136241.1:p.Gly334Arg
NP_001136242.1:p.Gly329Arg
NP_001136243.1:p.Gly334Arg
NP_001136244.1:p.Gly329Arg
NP_001136245.1:p.Gly307Arg
NP_001341333.1:p.Gly307Arg
NP_001341340.1:p.Gly329Arg
NP_001341349.1:p.Gly329Arg
NP_001341358.1:p.Gly329Arg
NP_001341359.1:p.Gly329Arg
NP_001371069.1:p.Gly329Arg
NP_149045.3:p.Gly329Arg
NC_000010.10:g.55996583C>T

Protein change:

G292R

Molecular consequence:

NM_001142763.2:c.1000G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001142764.2:c.985G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001142765.2:c.985G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001142766.2:c.985G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001142767.2:c.874G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001142768.2:c.919G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001142769.3:c.1000G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001142770.3:c.985G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001142771.2:c.1000G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001142772.2:c.985G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001142773.2:c.919G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001354404.2:c.919G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001354411.2:c.985G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001354420.2:c.985G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001354429.2:c.985G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001354430.2:c.985G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001384140.1:c.985G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_033056.4:c.985G>A - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Name:: Usher syndrome type 1F (USH1F)
Synonyms:: USHER SYNDROME, TYPE IF
Identifiers:: MONDO: MONDO:0011186; MedGen: C1865885; Orphanet: 231169; Orphanet: 886; OMIM: 602083

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV003761084	Broad Center for Mendelian Genomics, Broad Institute of MIT and Harvard	criteria provided, single submitter (ACMG Guidelines, 2015)	Uncertain significance (Jan 24, 2023)	germline	curation	PubMed (1) [See all records that cite this PMID]

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV003761084

Broad Center for Mendelian Genomics, Broad Institute of MIT and Harvard

criteria provided, single submitter

(ACMG Guidelines, 2015)

Uncertain significance
(Jan 24, 2023)

germline

curation

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	germline	unknown	not provided	not provided	not provided	not provided	not provided	curation

Citations

PubMed

Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology.

Richards S, Aziz N, Bale S, Bick D, Das S, Gastier-Foster J, Grody WW, Hegde M, Lyon E, Spector E, Voelkerding K, Rehm HL; ACMG Laboratory Quality Assurance Committee..

Genet Med. 2015 May;17(5):405-24. doi: 10.1038/gim.2015.30. Epub 2015 Mar 5.

PubMed [citation]

PMID:: 25741868
PMCID:: PMC4544753

Details of each submission

From Broad Center for Mendelian Genomics, Broad Institute of MIT and Harvard, SCV003761084.1

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

Description

The p.Gly329Arg variant in PCDH15 has been reported in 1 individual, in the homozygous state, with Usher syndrome type 1F (PMID: 26969326), and has been identified in 0.003% (1/34582) of Latino/Admixed American chromosomes by the Genome Aggregation Database (gnomAD, http://gnomad.broadinstitute.org; dbSNP ID: rs1166198215). Although this variant has been seen in the general population in a heterozygous state, its frequency is low enough to be consistent with a recessive carrier frequency. Computational prediction tools and conservation analyses suggest that this variant may impact the protein, though this information is not predictive enough to determine pathogenicity. In summary, while there is some suspicion for a pathogenic role, the clinical significance of this variant is uncertain. ACMG/AMP Criteria applied: PM2_supporting, PP3, PM3_supporting (Richards 2015).

#	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: Mar 30, 2024

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