NM_000264.5(PTCH1):c.2799del (p.Tyr934fs) AND Gorlin syndrome

This record was updated by the submitter. Please see the current version.

Germline classification:: Pathogenic (1 submission)
Last evaluated:: Mar 12, 2015
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:: RCV000199981.1

Allele description

NM_000264.5(PTCH1):c.2799del (p.Tyr934fs)

Gene:

PTCH1:patched 1 [Gene - OMIM - HGNC]

Variant type:

Deletion

Cytogenetic location:

9q22.32

Genomic location:

Preferred name:

NM_000264.5(PTCH1):c.2799del (p.Tyr934fs)

HGVS:

NC_000009.12:g.95459688del
NG_007664.1:g.62278del
NM_000264.5:c.2799delMANE SELECT
NM_001083602.3:c.2601del
NM_001083603.3:c.2796del
NM_001083604.3:c.2346del
NM_001083605.3:c.2346del
NM_001083606.3:c.2346del
NM_001083607.3:c.2346del
NM_001354918.2:c.2643del
NP_000255.2:p.Tyr934fs
NP_001077071.1:p.Tyr868fs
NP_001077072.1:p.Tyr933fs
NP_001077073.1:p.Tyr783fs
NP_001077074.1:p.Tyr783fs
NP_001077075.1:p.Tyr783fs
NP_001077076.1:p.Tyr783fs
NP_001341847.1:p.Tyr882fs
LRG_515t1:c.2799del
LRG_515:g.62278del
NC_000009.11:g.98221970del
NM_000264.3:c.2799delG
NR_149061.2:n.3538del

Protein change:

Y783fs

Links:

dbSNP: rs863224484

NCBI 1000 Genomes Browser:

rs863224484

Molecular consequence:

NM_000264.5:c.2799del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001083602.3:c.2601del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001083603.3:c.2796del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001083604.3:c.2346del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001083605.3:c.2346del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001083606.3:c.2346del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001083607.3:c.2346del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001354918.2:c.2643del - frameshift variant - [Sequence Ontology: SO:0001589]
NR_149061.2:n.3538del - non-coding transcript variant - [Sequence Ontology: SO:0001619]

Condition(s)

Name:: Gorlin syndrome (BCNS)
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: 109400

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000253818	Invitae	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Pathogenic (Mar 12, 2015)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000253818

Invitae

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Pathogenic
(Mar 12, 2015)

germline

clinical testing

PubMed (1)
[See all records that cite this PMID]

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

Sherloc: a comprehensive refinement of the ACMG-AMP variant classification criteria.

Nykamp K, Anderson M, Powers M, Garcia J, Herrera B, Ho YY, Kobayashi Y, Patil N, Thusberg J, Westbrook M; Invitae Clinical Genomics Group., Topper S.

Genet Med. 2017 Oct;19(10):1105-1117. doi: 10.1038/gim.2017.37. Epub 2017 May 11. Erratum in: Genet Med. 2020 Jan;22(1):240-242.

PubMed [citation]

PMID:: 28492532
PMCID:: PMC5632818

Details of each submission

From Invitae, SCV000253818.2

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

Description

This sequence change deletes 1 nucleotide from exon 17 of the PTCH1 mRNA (c.2799delG), causing a frameshift at codon 934. This creates a premature translational stop signal (p.Tyr934Metfs*28) and is expected to result in an absent or disrupted protein product. While this particular variant has not been reported in the literature, truncating variants in PTCH1 are known to be pathogenic (PMID: 16301862, 16419085). 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: Apr 23, 2022

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