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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Chain C, HEMOGLOBIN A (CARBONMONOXY) (ALPHA CHAIN)
Chain C, HEMOGLOBIN A (CARBONMONOXY) (ALPHA CHAIN)
gi|442663|pdb|1BBB|C

Protein

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV002647782	Ambry Genetics	criteria provided, single submitter (Ambry Variant Classification Scheme 2023)	Pathogenic (Mar 22, 2021)	germline	clinical testing	PubMed (7) [See all records that cite these PMIDs] 23761049, 26290144, 27680694, 29255261, 29792231, 29849051, 31113992 Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV002647782

Ambry Genetics

criteria provided, single submitter

(Ambry Variant Classification Scheme 2023)

Pathogenic
(Mar 22, 2021)

germline

clinical testing

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

Citation Link

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

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

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

#	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: May 1, 2024

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