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NM_000264.5(PTCH1):c.2408T>C (p.Met803Thr) AND Gorlin syndrome

Germline classification:
Uncertain significance (1 submission)
Last evaluated:
Jan 26, 2024
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:
RCV000544815.8

Allele description [Variation Report for NM_000264.5(PTCH1):c.2408T>C (p.Met803Thr)]

NM_000264.5(PTCH1):c.2408T>C (p.Met803Thr)

Genes:
PTCH1:patched 1 [Gene - OMIM - HGNC]
LOC100507346:uncharacterized LOC100507346 [Gene]
Variant type:
single nucleotide variant
Cytogenetic location:
9q22.32
Genomic location:
Preferred name:
NM_000264.5(PTCH1):c.2408T>C (p.Met803Thr)
HGVS:
  • NC_000009.12:g.95467268A>G
  • NG_007664.1:g.54698T>C
  • NM_000264.5:c.2408T>CMANE SELECT
  • NM_001083602.3:c.2210T>C
  • NM_001083603.3:c.2405T>C
  • NM_001083604.3:c.1955T>C
  • NM_001083605.3:c.1955T>C
  • NM_001083606.3:c.1955T>C
  • NM_001083607.3:c.1955T>C
  • NM_001354918.2:c.2252T>C
  • NP_000255.2:p.Met803Thr
  • NP_001077071.1:p.Met737Thr
  • NP_001077072.1:p.Met802Thr
  • NP_001077073.1:p.Met652Thr
  • NP_001077074.1:p.Met652Thr
  • NP_001077075.1:p.Met652Thr
  • NP_001077076.1:p.Met652Thr
  • NP_001341847.1:p.Met751Thr
  • LRG_515t1:c.2408T>C
  • LRG_515:g.54698T>C
  • NC_000009.11:g.98229550A>G
  • NM_000264.3:c.2408T>C
Protein change:
M652T
Links:
dbSNP: rs1554694376
NCBI 1000 Genomes Browser:
rs1554694376
Molecular consequence:
  • NM_000264.5:c.2408T>C - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001083602.3:c.2210T>C - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001083603.3:c.2405T>C - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001083604.3:c.1955T>C - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001083605.3:c.1955T>C - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001083606.3:c.1955T>C - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001083607.3:c.1955T>C - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001354918.2:c.2252T>C - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

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

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV000622960Labcorp Genetics (formerly Invitae), Labcorp
criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))		Uncertain significance
(Jan 26, 2024) 		germlineclinical testing

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

Help

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineunknownnot providednot providednot providednot providednot providedclinical 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. doi: 10.1038/s41436-019-0624-9.

PubMed [citation]
PMID:
28492532
PMCID:
PMC5632818

Details of each submission

From Labcorp Genetics (formerly Invitae), Labcorp, SCV000622960.7

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

Description

This sequence change replaces methionine, which is neutral and non-polar, with threonine, which is neutral and polar, at codon 803 of the PTCH1 protein (p.Met803Thr). This variant is not present in population databases (gnomAD no frequency). This variant has not been reported in the literature in individuals affected with PTCH1-related conditions. ClinVar contains an entry for this variant (Variation ID: 453823). Advanced modeling of protein sequence and biophysical properties (such as structural, functional, and spatial information, amino acid conservation, physicochemical variation, residue mobility, and thermodynamic stability) has been performed at Invitae for this missense variant, however the output from this modeling did not meet the statistical confidence thresholds required to predict the impact of this variant on PTCH1 protein function. In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance.

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

Last Updated: Sep 29, 2024