NM_001384140.1(PCDH15):c.1075C>T (p.Gln359Ter) AND not provided

Germline classification:: Pathogenic (1 submission)
Last evaluated:: Dec 21, 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:: RCV001244263.5

Allele description [Variation Report for NM_001384140.1(PCDH15):c.1075C>T (p.Gln359Ter)]

NM_001384140.1(PCDH15):c.1075C>T (p.Gln359Ter)

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.1075C>T (p.Gln359Ter)

HGVS:

NC_000010.11:g.54213959G>A
NG_009191.3:g.1420224C>T
NM_001142763.2:c.1090C>T
NM_001142764.2:c.1075C>T
NM_001142765.2:c.1075C>T
NM_001142766.2:c.1075C>T
NM_001142767.2:c.964C>T
NM_001142768.2:c.1009C>T
NM_001142769.3:c.1090C>T
NM_001142770.3:c.1075C>T
NM_001142771.2:c.1090C>T
NM_001142772.2:c.1075C>T
NM_001142773.2:c.1009C>T
NM_001354404.2:c.1009C>T
NM_001354411.2:c.1075C>T
NM_001354420.2:c.1075C>T
NM_001354429.2:c.1075C>T
NM_001354430.2:c.1075C>T
NM_001384140.1:c.1075C>TMANE SELECT
NM_033056.4:c.1075C>T
NP_001136235.1:p.Gln364Ter
NP_001136236.1:p.Gln359Ter
NP_001136237.1:p.Gln359Ter
NP_001136238.1:p.Gln359Ter
NP_001136239.1:p.Gln322Ter
NP_001136240.1:p.Gln337Ter
NP_001136241.1:p.Gln364Ter
NP_001136242.1:p.Gln359Ter
NP_001136243.1:p.Gln364Ter
NP_001136244.1:p.Gln359Ter
NP_001136245.1:p.Gln337Ter
NP_001341333.1:p.Gln337Ter
NP_001341340.1:p.Gln359Ter
NP_001341349.1:p.Gln359Ter
NP_001341358.1:p.Gln359Ter
NP_001341359.1:p.Gln359Ter
NP_001371069.1:p.Gln359Ter
NP_149045.3:p.Gln359Ter
NC_000010.10:g.55973719G>A
NM_033056.3:c.1075C>T

Protein change:

Q322*

Links:

dbSNP: rs2051720336

NCBI 1000 Genomes Browser:

rs2051720336

Molecular consequence:

NM_001142763.2:c.1090C>T - nonsense - [Sequence Ontology: SO:0001587]
NM_001142764.2:c.1075C>T - nonsense - [Sequence Ontology: SO:0001587]
NM_001142765.2:c.1075C>T - nonsense - [Sequence Ontology: SO:0001587]
NM_001142766.2:c.1075C>T - nonsense - [Sequence Ontology: SO:0001587]
NM_001142767.2:c.964C>T - nonsense - [Sequence Ontology: SO:0001587]
NM_001142768.2:c.1009C>T - nonsense - [Sequence Ontology: SO:0001587]
NM_001142769.3:c.1090C>T - nonsense - [Sequence Ontology: SO:0001587]
NM_001142770.3:c.1075C>T - nonsense - [Sequence Ontology: SO:0001587]
NM_001142771.2:c.1090C>T - nonsense - [Sequence Ontology: SO:0001587]
NM_001142772.2:c.1075C>T - nonsense - [Sequence Ontology: SO:0001587]
NM_001142773.2:c.1009C>T - nonsense - [Sequence Ontology: SO:0001587]
NM_001354404.2:c.1009C>T - nonsense - [Sequence Ontology: SO:0001587]
NM_001354411.2:c.1075C>T - nonsense - [Sequence Ontology: SO:0001587]
NM_001354420.2:c.1075C>T - nonsense - [Sequence Ontology: SO:0001587]
NM_001354429.2:c.1075C>T - nonsense - [Sequence Ontology: SO:0001587]
NM_001354430.2:c.1075C>T - nonsense - [Sequence Ontology: SO:0001587]
NM_001384140.1:c.1075C>T - nonsense - [Sequence Ontology: SO:0001587]
NM_033056.4:c.1075C>T - nonsense - [Sequence Ontology: SO:0001587]

Condition(s)

Synonyms:: none provided
Identifiers:: MedGen: C3661900

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV001417471	Invitae	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Pathogenic (Dec 21, 2023)	germline	clinical testing	PubMed (4) [See all records that cite these PMIDs] 11398101, 11487575, 14570705, 28492532

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV001417471

Invitae

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Pathogenic
(Dec 21, 2023)

germline

clinical testing

PubMed (4)
[See all records that cite these PMIDs]

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

Citations

PubMed

Mutations of the protocadherin gene PCDH15 cause Usher syndrome type 1F.

Ahmed ZM, Riazuddin S, Bernstein SL, Ahmed Z, Khan S, Griffith AJ, Morell RJ, Friedman TB, Riazuddin S, Wilcox ER.

Am J Hum Genet. 2001 Jul;69(1):25-34. Epub 2001 Jun 7.

PubMed [citation]

PMID:: 11398101
PMCID:: PMC1226045

Mutations in the novel protocadherin PCDH15 cause Usher syndrome type 1F.

Alagramam KN, Yuan H, Kuehn MH, Murcia CL, Wayne S, Srisailpathy CR, Lowry RB, Knaus R, Van Laer L, Bernier FP, Schwartz S, Lee C, Morton CC, Mullins RF, Ramesh A, Van Camp G, Hageman GS, Woychik RP, Smith RJ.

Hum Mol Genet. 2001 Aug 1;10(16):1709-18. Erratum in: Hum Mol Genet 2001 Oct 15;10(22):2603. Hagemen GS [corrected to Hageman GS].

PubMed [citation]

PMID:: 11487575

See all PubMed Citations (4)

Details of each submission

From Invitae, SCV001417471.5

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (4)

Description

This sequence change creates a premature translational stop signal (p.Gln359*) in the PCDH15 gene. It is expected to result in an absent or disrupted protein product. Loss-of-function variants in PCDH15 are known to be pathogenic (PMID: 11398101, 11487575, 14570705). This variant is not present in population databases (gnomAD no frequency). This variant has not been reported in the literature in individuals affected with PCDH15-related conditions. ClinVar contains an entry for this variant (Variation ID: 969009). For these reasons, this variant has been classified as 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: Feb 28, 2024

ClinVar

Relating variation to medicine