U.S. flag

An official website of the United States government

NM_001384140.1(PCDH15):c.4671+1559C>T AND not specified

Germline classification:
Uncertain significance (1 submission)
Last evaluated:
Feb 25, 2019
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:
RCV001002355.15

Allele description [Variation Report for NM_001384140.1(PCDH15):c.4671+1559C>T]

NM_001384140.1(PCDH15):c.4671+1559C>T

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.4671+1559C>T
HGVS:
  • NC_000010.11:g.53808997G>A
  • NG_009191.3:g.1825186C>T
  • NM_001142769.3:c.5068C>T
  • NM_001142770.3:c.*483C>T
  • NM_001142771.2:c.4497+1559C>T
  • NM_001142772.2:c.4482+1559C>T
  • NM_001354411.2:c.5047C>T
  • NM_001354420.2:c.4476+1559C>T
  • NM_001354429.2:c.4605+1559C>T
  • NM_001384140.1:c.4671+1559C>TMANE SELECT
  • NP_001136241.1:p.Gln1690Ter
  • NP_001341340.1:p.Gln1683Ter
  • NC_000010.10:g.55568757G>A
  • NM_033056.3:c.*12861C>T
Protein change:
Q1683*
Links:
dbSNP: rs368397508
NCBI 1000 Genomes Browser:
rs368397508
Molecular consequence:
  • NM_001142770.3:c.*483C>T - 3 prime UTR variant - [Sequence Ontology: SO:0001624]
  • NM_001142771.2:c.4497+1559C>T - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001142772.2:c.4482+1559C>T - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001354420.2:c.4476+1559C>T - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001354429.2:c.4605+1559C>T - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001384140.1:c.4671+1559C>T - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001142769.3:c.5068C>T - nonsense - [Sequence Ontology: SO:0001587]
  • NM_001354411.2:c.5047C>T - nonsense - [Sequence Ontology: SO:0001587]

Condition(s)

Synonyms:
AllHighlyPenetrant
Identifiers:
MedGen: CN169374

Recent activity

Clear Turn Off Turn On

Your browsing activity is empty.

Activity recording is turned off.

Turn recording back on

See more...

Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV001160260ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories
criteria provided, single submitter

(ARUP Molecular Germline Variant Investigation Process)		Uncertain significance
(Feb 25, 2019) 		germlineclinical testing

Citation Link

Help

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineunknownnot providednot providednot providednot providednot providedclinical testing

Details of each submission

From ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories, SCV001160260.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testingnot provided

Description

The PCDH15 c.5068C>T; p.Gln1690Ter variant (rs368397508), to our knowledge, has not been reported in the medical literature; however, this variant is listed in the ClinVar database as a variant of uncertain significance (Variation ID: 553502; reported as NM_033056.3(PCDH15):c.*12861C>T). This variant introduces an early termination codon in the terminal exon (37/37) of the NM_001142769.1 (CD2.1) transcript, which may not lead to nonsense-mediated decay, and it is expected to truncate the mature peptide by 6%. When annotated using the NM_033056.3 transcript (which encodes the longest peptide), this variant is positioned downstream of the 3' UTR. The c.5068C>T variant is found in the non-Finnish European population with an allele frequency of 0.004% (3/75,182 alleles) in the Genome Aggregation Database. Due to limited information, the clinical significance of this variant is uncertain.

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknownnot providednot providednot providednot providednot providednot providednot provided

Last Updated: May 7, 2024