NM_000264.5(PTCH1):c.3410_3424del (p.Val1137_Ala1141del) AND Hereditary cancer-predisposing syndrome

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Jun 29, 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:: RCV000492738.3

Allele description [Variation Report for NM_000264.5(PTCH1):c.3410_3424del (p.Val1137_Ala1141del)]

NM_000264.5(PTCH1):c.3410_3424del (p.Val1137_Ala1141del)

Gene:

PTCH1:patched 1 [Gene - OMIM - HGNC]

Variant type:

Deletion

Cytogenetic location:

9q22.32

Genomic location:

Preferred name:

NM_000264.5(PTCH1):c.3410_3424del (p.Val1137_Ala1141del)

HGVS:

NC_000009.12:g.95453504_95453518del
NG_007664.1:g.68449_68463del
NM_000264.5:c.3410_3424delMANE SELECT
NM_001083602.3:c.3212_3226del
NM_001083603.3:c.3407_3421del
NM_001083604.3:c.2957_2971del
NM_001083605.3:c.2957_2971del
NM_001083606.3:c.2957_2971del
NM_001083607.3:c.2957_2971del
NM_001354918.2:c.3254_3268del
NP_000255.2:p.Val1137_Ala1141del
NP_001077071.1:p.Val1071_Ala1075del
NP_001077072.1:p.Val1136_Ala1140del
NP_001077073.1:p.Val986_Ala990del
NP_001077074.1:p.Val986_Ala990del
NP_001077075.1:p.Val986_Ala990del
NP_001077076.1:p.Val986_Ala990del
NP_001341847.1:p.Val1085_Ala1089del
LRG_515:g.68449_68463del
NC_000009.11:g.98215786_98215800del
NR_149061.2:n.4149_4163del

Links:

dbSNP: rs1554690414

NCBI 1000 Genomes Browser:

rs1554690414

Molecular consequence:

NM_000264.5:c.3410_3424del - inframe_deletion - [Sequence Ontology: SO:0001822]
NM_001083602.3:c.3212_3226del - inframe_deletion - [Sequence Ontology: SO:0001822]
NM_001083603.3:c.3407_3421del - inframe_deletion - [Sequence Ontology: SO:0001822]
NM_001083604.3:c.2957_2971del - inframe_deletion - [Sequence Ontology: SO:0001822]
NM_001083605.3:c.2957_2971del - inframe_deletion - [Sequence Ontology: SO:0001822]
NM_001083606.3:c.2957_2971del - inframe_deletion - [Sequence Ontology: SO:0001822]
NM_001083607.3:c.2957_2971del - inframe_deletion - [Sequence Ontology: SO:0001822]
NM_001354918.2:c.3254_3268del - inframe_deletion - [Sequence Ontology: SO:0001822]
NR_149061.2:n.4149_4163del - non-coding transcript variant - [Sequence Ontology: SO:0001619]

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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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000581039	Ambry Genetics	criteria provided, single submitter (Ambry Variant Classification Scheme 2023)	Uncertain significance (Jun 29, 2015)	germline	clinical testing	Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000581039

Ambry Genetics

criteria provided, single submitter

(Ambry Variant Classification Scheme 2023)

Uncertain significance
(Jun 29, 2015)

germline

clinical testing

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

Details of each submission

From Ambry Genetics, SCV000581039.6

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

Description

The c.3410_3424del15 variant is located in coding exon 20 of the PTCH1 gene. This variant results from an in-frame TGCTGATGCTGGCGG deletion of 15 nucleotides between nucleotide positions 3410 and 3424. This variant was not reported in population based cohorts in the following databases: Database of Single Nucleotide Polymorphisms (dbSNP), NHLBI Exome Sequencing Project (ESP), and 1000 Genomes Project. In the ESP, this variant was not observed in 6503 samples (13006 alleles) with coverage at this position. To date, this alteration has been detected with an allele frequency of approximately 0.47% (greater than 200 alleles tested) in our clinical cohort. These nucleotide positions are not well conserved in available vertebrate species. Since supporting evidence is limited at this time, the clinical significance of c.3410_3424del15 remains unclear.

#	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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