NM_001384140.1(PCDH15):c.3112G>T (p.Glu1038Ter) AND Usher syndrome type 1D

Germline classification:: Likely pathogenic (1 submission)
Last evaluated:: Feb 28, 2022
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:: RCV002307868.2

Allele description [Variation Report for NM_001384140.1(PCDH15):c.3112G>T (p.Glu1038Ter)]

NM_001384140.1(PCDH15):c.3112G>T (p.Glu1038Ter)

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.3112G>T (p.Glu1038Ter)

HGVS:

NC_000010.11:g.53959742C>A
NG_009191.3:g.1674441G>T
NM_001142763.2:c.3127G>T
NM_001142764.2:c.3112G>T
NM_001142765.2:c.2899G>T
NM_001142766.2:c.3112G>T
NM_001142767.2:c.3001G>T
NM_001142768.2:c.3046G>T
NM_001142769.3:c.3148G>T
NM_001142770.3:c.3112G>T
NM_001142771.2:c.3127G>T
NM_001142772.2:c.3112G>T
NM_001142773.2:c.3046G>T
NM_001354404.2:c.3046G>T
NM_001354411.2:c.3133G>T
NM_001354420.2:c.3112G>T
NM_001354429.2:c.3112G>T
NM_001384140.1:c.3112G>TMANE SELECT
NM_033056.4:c.3112G>T
NP_001136235.1:p.Glu1043Ter
NP_001136236.1:p.Glu1038Ter
NP_001136237.1:p.Glu967Ter
NP_001136238.1:p.Glu1038Ter
NP_001136239.1:p.Glu1001Ter
NP_001136240.1:p.Glu1016Ter
NP_001136241.1:p.Glu1050Ter
NP_001136242.1:p.Glu1038Ter
NP_001136243.1:p.Glu1043Ter
NP_001136244.1:p.Glu1038Ter
NP_001136245.1:p.Glu1016Ter
NP_001341333.1:p.Glu1016Ter
NP_001341340.1:p.Glu1045Ter
NP_001341349.1:p.Glu1038Ter
NP_001341358.1:p.Glu1038Ter
NP_001371069.1:p.Glu1038Ter
NP_149045.3:p.Glu1038Ter
NC_000010.10:g.55719502C>A

Protein change:

E1001*

Molecular consequence:

NM_001142763.2:c.3127G>T - nonsense - [Sequence Ontology: SO:0001587]
NM_001142764.2:c.3112G>T - nonsense - [Sequence Ontology: SO:0001587]
NM_001142765.2:c.2899G>T - nonsense - [Sequence Ontology: SO:0001587]
NM_001142766.2:c.3112G>T - nonsense - [Sequence Ontology: SO:0001587]
NM_001142767.2:c.3001G>T - nonsense - [Sequence Ontology: SO:0001587]
NM_001142768.2:c.3046G>T - nonsense - [Sequence Ontology: SO:0001587]
NM_001142769.3:c.3148G>T - nonsense - [Sequence Ontology: SO:0001587]
NM_001142770.3:c.3112G>T - nonsense - [Sequence Ontology: SO:0001587]
NM_001142771.2:c.3127G>T - nonsense - [Sequence Ontology: SO:0001587]
NM_001142772.2:c.3112G>T - nonsense - [Sequence Ontology: SO:0001587]
NM_001142773.2:c.3046G>T - nonsense - [Sequence Ontology: SO:0001587]
NM_001354404.2:c.3046G>T - nonsense - [Sequence Ontology: SO:0001587]
NM_001354411.2:c.3133G>T - nonsense - [Sequence Ontology: SO:0001587]
NM_001354420.2:c.3112G>T - nonsense - [Sequence Ontology: SO:0001587]
NM_001354429.2:c.3112G>T - nonsense - [Sequence Ontology: SO:0001587]
NM_001384140.1:c.3112G>T - nonsense - [Sequence Ontology: SO:0001587]
NM_033056.4:c.3112G>T - nonsense - [Sequence Ontology: SO:0001587]

Condition(s)

Name:: Usher syndrome type 1D (USH1D)
Synonyms:: USHER SYNDROME, TYPE ID
Identifiers:: MONDO: MONDO:0010984; MedGen: C1832845; Orphanet: 231169; Orphanet: 886; OMIM: 601067

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV002604328	Myriad Genetics, Inc.	criteria provided, single submitter (Myriad Women's Health Autosomal Recessive and X-Linked Classification Criteria (2021))	Likely pathogenic (Feb 28, 2022)	unknown	clinical testing	Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV002604328

Myriad Genetics, Inc.

criteria provided, single submitter

(Myriad Women's Health Autosomal Recessive and X-Linked Classification Criteria (2021))

Likely pathogenic
(Feb 28, 2022)

unknown

clinical testing

Citation Link

Help

Summary from all submissions

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

Details of each submission

From Myriad Genetics, Inc., SCV002604328.2

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

Description

NM_033056.3(PCDH15):c.3112G>T(E1038*) is expected to be pathogenic in the context of PCDH15-related disorders. This variant is predicted to lead to an abnormal or absent protein product due to the creation of a premature termination codon in PCDH15, a gene where loss-of-function variants are known to be pathogenic. Please note: this variant was assessed in the context of healthy population screening.

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	unknown	unknown	not provided	not provided	not provided		not provided	not provided	not provided	not provided

Last Updated: Dec 24, 2022

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