NM_000264.5(PTCH1):c.590G>A (p.Trp197Ter) AND Gorlin syndrome

Germline classification:: Pathogenic (1 submission)
Last evaluated:: May 19, 2018
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:: RCV000551617.6

Allele description [Variation Report for NM_000264.5(PTCH1):c.590G>A (p.Trp197Ter)]

NM_000264.5(PTCH1):c.590G>A (p.Trp197Ter)

Gene:

PTCH1:patched 1 [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

9q22.32

Genomic location:

Preferred name:

NM_000264.5(PTCH1):c.590G>A (p.Trp197Ter)

HGVS:

NC_000009.12:g.95482198C>T
NG_007664.1:g.39768G>A
NM_000264.5:c.590G>AMANE SELECT
NM_001083602.3:c.392G>A
NM_001083603.3:c.587G>A
NM_001083604.3:c.137G>A
NM_001083605.3:c.137G>A
NM_001083606.3:c.137G>A
NM_001083607.3:c.137G>A
NM_001354918.2:c.590G>A
NM_001354919.2:c.392G>A
NP_000255.2:p.Trp197Ter
NP_001077071.1:p.Trp131Ter
NP_001077072.1:p.Trp196Ter
NP_001077073.1:p.Trp46Ter
NP_001077074.1:p.Trp46Ter
NP_001077075.1:p.Trp46Ter
NP_001077076.1:p.Trp46Ter
NP_001341847.1:p.Trp197Ter
NP_001341848.1:p.Trp131Ter
LRG_515t1:c.590G>A
LRG_515:g.39768G>A
NC_000009.11:g.98244480C>T
NM_000264.3:c.590G>A
NR_149061.2:n.1495G>A

Protein change:

W131*

Links:

dbSNP: rs1064793922

NCBI 1000 Genomes Browser:

rs1064793922

Molecular consequence:

NR_149061.2:n.1495G>A - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NM_000264.5:c.590G>A - nonsense - [Sequence Ontology: SO:0001587]
NM_001083602.3:c.392G>A - nonsense - [Sequence Ontology: SO:0001587]
NM_001083603.3:c.587G>A - nonsense - [Sequence Ontology: SO:0001587]
NM_001083604.3:c.137G>A - nonsense - [Sequence Ontology: SO:0001587]
NM_001083605.3:c.137G>A - nonsense - [Sequence Ontology: SO:0001587]
NM_001083606.3:c.137G>A - nonsense - [Sequence Ontology: SO:0001587]
NM_001083607.3:c.137G>A - nonsense - [Sequence Ontology: SO:0001587]
NM_001354918.2:c.590G>A - nonsense - [Sequence Ontology: SO:0001587]
NM_001354919.2:c.392G>A - nonsense - [Sequence Ontology: SO:0001587]

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
SCV000623052	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Pathogenic (May 19, 2018)	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

SCV000623052

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Pathogenic
(May 19, 2018)

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, SCV000623052.5

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

Description

This sequence change creates a premature translational stop signal (p.Trp197*) in the PTCH1 gene. It is expected to result in an absent or disrupted protein product. This variant is not present in population databases (ExAC no frequency). This variant has not been reported in the literature in individuals with PTCH1-related disease. ClinVar contains an entry for this variant (Variation ID: 419509). Loss-of-function 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: Sep 29, 2024

ClinVar

Relating variation to medicine