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NM_000264.5(PTCH1):c.1247C>G (p.Thr416Ser) AND Hereditary cancer-predisposing syndrome

Germline classification:
Likely benign (2 submissions)
Last evaluated:
Nov 25, 2021
Review status:
2 stars out of maximum of 4 stars
criteria provided, multiple submitters, no conflicts
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:
RCV001010538.4

Allele description [Variation Report for NM_000264.5(PTCH1):c.1247C>G (p.Thr416Ser)]

NM_000264.5(PTCH1):c.1247C>G (p.Thr416Ser)

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.1247C>G (p.Thr416Ser)
HGVS:
  • NC_000009.12:g.95478155G>C
  • NG_007664.1:g.43811C>G
  • NM_000264.5:c.1247C>GMANE SELECT
  • NM_001083602.3:c.1049C>G
  • NM_001083603.3:c.1244C>G
  • NM_001083604.3:c.794C>G
  • NM_001083605.3:c.794C>G
  • NM_001083606.3:c.794C>G
  • NM_001083607.3:c.794C>G
  • NM_001354918.2:c.1247C>G
  • NP_000255.2:p.Thr416Ser
  • NP_001077071.1:p.Thr350Ser
  • NP_001077072.1:p.Thr415Ser
  • NP_001077073.1:p.Thr265Ser
  • NP_001077074.1:p.Thr265Ser
  • NP_001077075.1:p.Thr265Ser
  • NP_001077076.1:p.Thr265Ser
  • NP_001341847.1:p.Thr416Ser
  • LRG_515t1:c.1247C>G
  • LRG_515:g.43811C>G
  • NC_000009.11:g.98240437G>C
  • NM_000264.3:c.1247C>G
  • NM_000264.4:c.1247C>G
  • NR_149061.2:n.2152C>G
Protein change:
T265S
Links:
dbSNP: rs201174718
NCBI 1000 Genomes Browser:
rs201174718
Molecular consequence:
  • NM_000264.5:c.1247C>G - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001083602.3:c.1049C>G - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001083603.3:c.1244C>G - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001083604.3:c.794C>G - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001083605.3:c.794C>G - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001083606.3:c.794C>G - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001083607.3:c.794C>G - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001354918.2:c.1247C>G - missense variant - [Sequence Ontology: SO:0001583]
  • NR_149061.2:n.2152C>G - 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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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV001170754Ambry Genetics
criteria provided, single submitter

(Ambry Variant Classification Scheme 2023)
Likely benign
(Apr 2, 2021)
germlineclinical testing

PubMed (2)
[See all records that cite these PMIDs]

Citation Link,

SCV002526801Sema4, Sema4
criteria provided, single submitter

(Sema4 Curation Guidelines)
Likely benign
(Nov 25, 2021)
germlinecuration

Citation Link

Summary from all submissions

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

Citations

PubMed

Mechanisms of inactivation of PTCH1 gene in nevoid basal cell carcinoma syndrome: modification of the two-hit hypothesis.

Pan S, Dong Q, Sun LS, Li TJ.

Clin Cancer Res. 2010 Jan 15;16(2):442-50. doi: 10.1158/1078-0432.CCR-09-2574. Epub 2010 Jan 12.

PubMed [citation]
PMID:
20068110

Whole exome sequencing implicates PTCH1 and COL17A1 genes in ossification of the posterior longitudinal ligament of the cervical spine in Chinese patients.

Wei W, He HL, Chen CY, Zhao Y, Jiang HL, Liu WT, Du ZF, Chen XL, Shi SY, Zhang XN.

Genet Mol Res. 2014 Mar 17;13(1):1794-804. doi: 10.4238/2014.March.17.7.

PubMed [citation]
PMID:
24668667

Details of each submission

From Ambry Genetics, SCV001170754.4

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (2)

Description

This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity.

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

From Sema4, Sema4, SCV002526801.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedcurationnot provided
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknownnot providednot providednot providednot providednot providednot providednot provided

Last Updated: Jul 7, 2024