NM_000264.5(PTCH1):c.3441_3444del (p.Phe1147fs) AND Gorlin syndrome

Germline classification:: Pathogenic (1 submission)
Last evaluated:: Feb 5, 2020
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:: RCV001384649.7

Allele description [Variation Report for NM_000264.5(PTCH1):c.3441_3444del (p.Phe1147fs)]

NM_000264.5(PTCH1):c.3441_3444del (p.Phe1147fs)

Gene:

PTCH1:patched 1 [Gene - OMIM - HGNC]

Variant type:

Deletion

Cytogenetic location:

9q22.32

Genomic location:

Preferred name:

NM_000264.5(PTCH1):c.3441_3444del (p.Phe1147fs)

HGVS:

NC_000009.12:g.95453485_95453488del
NG_007664.1:g.68480_68483del
NM_000264.5:c.3441_3444delMANE SELECT
NM_001083602.3:c.3243_3246del
NM_001083603.3:c.3438_3441del
NM_001083604.3:c.2988_2991del
NM_001083605.3:c.2988_2991del
NM_001083606.3:c.2988_2991del
NM_001083607.3:c.2988_2991del
NM_001354918.2:c.3285_3288del
NP_000255.2:p.Phe1147fs
NP_001077071.1:p.Phe1081fs
NP_001077072.1:p.Phe1146fs
NP_001077073.1:p.Phe996fs
NP_001077074.1:p.Phe996fs
NP_001077075.1:p.Phe996fs
NP_001077076.1:p.Phe996fs
NP_001341847.1:p.Phe1095fs
LRG_515:g.68480_68483del
NC_000009.11:g.98215765_98215768del
NC_000009.11:g.98215767_98215770del
NR_149061.2:n.4180_4183del

Protein change:

F1081fs

Links:

dbSNP: rs2136630846

NCBI 1000 Genomes Browser:

rs2136630846

Molecular consequence:

NM_000264.5:c.3441_3444del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001083602.3:c.3243_3246del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001083603.3:c.3438_3441del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001083604.3:c.2988_2991del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001083605.3:c.2988_2991del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001083606.3:c.2988_2991del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001083607.3:c.2988_2991del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001354918.2:c.3285_3288del - frameshift variant - [Sequence Ontology: SO:0001589]
NR_149061.2:n.4180_4183del - non-coding transcript variant - [Sequence Ontology: SO:0001619]

Condition(s)

Name:: Gorlin syndrome
Synonyms:: Basal cell nevus syndrome
Identifiers:: MONDO: MONDO:0007187; MedGen: C0004779; Orphanet: 377; OMIM: PS109400

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV001584221	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Pathogenic (Feb 5, 2020)	germline	clinical testing	PubMed (3) [See all records that cite these PMIDs] 16301862, 16419085, 28492532

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV001584221

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Pathogenic
(Feb 5, 2020)

germline

clinical testing

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

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

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 Labcorp Genetics (formerly Invitae), Labcorp, SCV001584221.5

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (3)

Description

For these reasons, this variant has been classified as Pathogenic. Loss-of-function variants in PTCH1 are known to be pathogenic (PMID: 16301862, 16419085). This variant has not been reported in the literature in individuals with PTCH1-related conditions. This variant is not present in population databases (ExAC no frequency). This sequence change creates a premature translational stop signal (p.Phe1147Leufs*43) in the PTCH1 gene. It is expected to result in an absent or disrupted protein product.

#	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: Sep 29, 2024

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