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NM_000264.5(PTCH1):c.3307-115_3339del AND Gorlin syndrome

Germline classification:
Likely pathogenic (1 submission)
Last evaluated:
Aug 29, 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:
RCV001209501.5

Allele description [Variation Report for NM_000264.5(PTCH1):c.3307-115_3339del]

NM_000264.5(PTCH1):c.3307-115_3339del

Gene:
PTCH1:patched 1 [Gene - OMIM - HGNC]
Variant type:
Deletion
Cytogenetic location:
9q22.32
Genomic location:
Preferred name:
NM_000264.5(PTCH1):c.3307-115_3339del
HGVS:
  • NC_000009.12:g.95453588_95453735del
  • NG_007664.1:g.68231_68378del
  • NM_000264.5:c.3307-115_3339delMANE SELECT
  • NM_001083602.3:c.3109-115_3141del
  • NM_001083603.3:c.3304-115_3336del
  • NM_001083604.3:c.2854-115_2886del
  • NM_001083605.3:c.2854-115_2886del
  • NM_001083606.3:c.2854-115_2886del
  • NM_001083607.3:c.2854-115_2886del
  • NM_001354918.2:c.3151-115_3183del
  • LRG_515t1:c.3307-115_3339del
  • LRG_515:g.68231_68378del
  • NC_000009.11:g.98215870_98216017del
  • NM_000264.3:c.3307-115_3339del
Links:
dbSNP: rs1838664702
NCBI 1000 Genomes Browser:
rs1838664702
Molecular consequence:
  • NM_000264.5:c.3307-115_3339del - splice acceptor variant - [Sequence Ontology: SO:0001574]
  • NM_001083602.3:c.3109-115_3141del - splice acceptor variant - [Sequence Ontology: SO:0001574]
  • NM_001083603.3:c.3304-115_3336del - splice acceptor variant - [Sequence Ontology: SO:0001574]
  • NM_001083604.3:c.2854-115_2886del - splice acceptor variant - [Sequence Ontology: SO:0001574]
  • NM_001083605.3:c.2854-115_2886del - splice acceptor variant - [Sequence Ontology: SO:0001574]
  • NM_001083606.3:c.2854-115_2886del - splice acceptor variant - [Sequence Ontology: SO:0001574]
  • NM_001083607.3:c.2854-115_2886del - splice acceptor variant - [Sequence Ontology: SO:0001574]
  • NM_001354918.2:c.3151-115_3183del - splice acceptor variant - [Sequence Ontology: SO:0001574]

Condition(s)

Name:
Gorlin syndrome
Synonyms:
Gorlin-Goltz Syndrome; Multiple Basal Cell Nevi, Odontogenic Keratocysts, And Skeletal Anomalies; Fifth Phacomatosis; See all synonyms [MedGen]
Identifiers:
MONDO: MONDO:0007187; MedGen: C0004779; Orphanet: 377; OMIM: PS109400

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV001380938Invitae
criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))		Likely pathogenic
(Aug 29, 2019) 		germlineclinical testing

PubMed (3)
[See all records that cite these PMIDs]

Help

Summary from all submissions

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

Citations

PubMed

Clinical testing for the nevoid basal cell carcinoma syndrome in a DNA diagnostic laboratory.

Klein RD, Dykas DJ, Bale AE.

Genet Med. 2005 Nov-Dec;7(9):611-9.

PubMed [citation]
PMID:
16301862

PTCH mutations: distribution and analyses.

Lindström E, Shimokawa T, Toftgård R, Zaphiropoulos PG.

Hum Mutat. 2006 Mar;27(3):215-9. Review.

PubMed [citation]
PMID:
16419085
See all PubMed Citations (3)

Details of each submission

From Invitae, SCV001380938.5

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (3)

Description

This variant has not been reported in the literature in individuals with PTCH1-related conditions. In summary, the currently available evidence indicates that the variant is pathogenic, but additional data are needed to prove that conclusively. Therefore, this variant has been classified as Likely Pathogenic. Loss-of-function variants in PTCH1 are known to be pathogenic (PMID: 16301862, 16419085). This variant results in the deletion of part of exon 20 (c.3307-115_3339del) of the PTCH1 gene. It is expected to disrupt RNA splicing and likely results in an absent or disrupted protein product.

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

Last Updated: Feb 20, 2024