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NM_000264.5(PTCH1):c.585-15_586del AND Hereditary cancer-predisposing syndrome

Germline classification:
Pathogenic (1 submission)
Last evaluated:
Mar 22, 2021
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:
RCV002353344.2

Allele description [Variation Report for NM_000264.5(PTCH1):c.585-15_586del]

NM_000264.5(PTCH1):c.585-15_586del

Gene:
PTCH1:patched 1 [Gene - OMIM - HGNC]
Variant type:
Deletion
Cytogenetic location:
9q22.32
Genomic location:
Preferred name:
NM_000264.5(PTCH1):c.585-15_586del
HGVS:
  • NC_000009.12:g.95482204_95482220del
  • NG_007664.1:g.39748_39764del
  • NM_000264.5:c.585-15_586delMANE SELECT
  • NM_001083602.3:c.387-15_388del
  • NM_001083603.3:c.582-15_583del
  • NM_001083604.3:c.132-15_133del
  • NM_001083605.3:c.132-15_133del
  • NM_001083606.3:c.132-15_133del
  • NM_001083607.3:c.132-15_133del
  • NM_001354918.2:c.585-15_586del
  • NM_001354919.2:c.387-15_388del
  • LRG_515t1:c.585-15_586del17
  • LRG_515:g.39748_39764del
  • NC_000009.11:g.98244486_98244502del
  • NM_000264.3:c.585-15_586del17
Molecular consequence:
  • NM_000264.5:c.585-15_586del - splice acceptor variant - [Sequence Ontology: SO:0001574]
  • NM_001083602.3:c.387-15_388del - splice acceptor variant - [Sequence Ontology: SO:0001574]
  • NM_001083603.3:c.582-15_583del - splice acceptor variant - [Sequence Ontology: SO:0001574]
  • NM_001083604.3:c.132-15_133del - splice acceptor variant - [Sequence Ontology: SO:0001574]
  • NM_001083605.3:c.132-15_133del - splice acceptor variant - [Sequence Ontology: SO:0001574]
  • NM_001083606.3:c.132-15_133del - splice acceptor variant - [Sequence Ontology: SO:0001574]
  • NM_001083607.3:c.132-15_133del - splice acceptor variant - [Sequence Ontology: SO:0001574]
  • NM_001354918.2:c.585-15_586del - splice acceptor variant - [Sequence Ontology: SO:0001574]
  • NM_001354919.2:c.387-15_388del - splice acceptor variant - [Sequence Ontology: SO:0001574]

Condition(s)

Name:
Hereditary cancer-predisposing syndrome
Synonyms:
Neoplastic Syndromes, Hereditary; Tumor predisposition; Cancer predisposition; See all synonyms [MedGen]
Identifiers:
MONDO: MONDO:0015356; MeSH: D009386; MedGen: C0027672

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV002647782Ambry Genetics
criteria provided, single submitter

(Ambry Variant Classification Scheme 2023)		Pathogenic
(Mar 22, 2021) 		germlineclinical testing

PubMed (7)
[See all records that cite these PMIDs]

Citation Link

Help

Summary from all submissions

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

Citations

PubMed

Association between PTCH1 polymorphisms and risk of neural tube defects in a Chinese population.

Wang Z, Wang L, Shangguan S, Lu X, Chang S, Wang J, Zou J, Wu L, Zhang T, Luo Y.

Birth Defects Res A Clin Mol Teratol. 2013 Jun;97(6):409-15. doi: 10.1002/bdra.23152. Epub 2013 Jun 13.

PubMed [citation]
PMID:
23761049

CCND2, CTNNB1, DDX3X, GLI2, SMARCA4, MYC, MYCN, PTCH1, TP53, and MLL2 gene variants and risk of childhood medulloblastoma.

Dahlin AM, Hollegaard MV, Wibom C, Andersson U, Hougaard DM, Deltour I, Hjalmars U, Melin B.

J Neurooncol. 2015 Oct;125(1):75-8. doi: 10.1007/s11060-015-1891-1. Epub 2015 Aug 20.

PubMed [citation]
PMID:
26290144
PMCID:
PMC4592490
See all PubMed Citations (7)

Details of each submission

From Ambry Genetics, SCV002647782.2

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (7)

Description

The c.585-15_586del17 pathogenic mutation results from a deletion of 17 nucleotides between positions c.585-15 and c.586 and involves the canonical splice acceptor site before coding exon 4 of the PTCH1 gene. The canonical splice acceptor site is well conserved in available vertebrate species. Using the BDGP and ESEfinder splice site prediction tools, this alteration is predicted to abolish the native acceptor splice site; however, direct evidence is unavailable. Alterations that disrupt the canonical splice site are expected to cause aberrant splicing, resulting in an abnormal protein or a transcript that is subject to nonsense-mediated mRNA decay. As such, this alteration is interpreted as a disease-causing mutation.

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

Last Updated: May 1, 2024