NM_000264.5(PTCH1):c.1177G>A (p.Ala393Thr) AND Gorlin syndrome

Germline classification:: Benign (2 submissions)
Last evaluated:: Jan 25, 2024
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:: RCV000532256.14

Allele description [Variation Report for NM_000264.5(PTCH1):c.1177G>A (p.Ala393Thr)]

NM_000264.5(PTCH1):c.1177G>A (p.Ala393Thr)

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.1177G>A (p.Ala393Thr)

HGVS:

NC_000009.12:g.95479038C>T
NG_007664.1:g.42928G>A
NM_000264.5:c.1177G>AMANE SELECT
NM_001083602.3:c.979G>A
NM_001083603.3:c.1174G>A
NM_001083604.3:c.724G>A
NM_001083605.3:c.724G>A
NM_001083606.3:c.724G>A
NM_001083607.3:c.724G>A
NM_001354918.2:c.1177G>A
NP_000255.2:p.Ala393Thr
NP_001077071.1:p.Ala327Thr
NP_001077072.1:p.Ala392Thr
NP_001077073.1:p.Ala242Thr
NP_001077074.1:p.Ala242Thr
NP_001077075.1:p.Ala242Thr
NP_001077076.1:p.Ala242Thr
NP_001341847.1:p.Ala393Thr
LRG_515t1:c.1177G>A
LRG_515:g.42928G>A
NC_000009.11:g.98241320C>T
NM_000264.3:c.1177G>A
NR_149061.2:n.2082G>A
Q13635:p.Ala393Thr

Protein change:

A242T; ALA393THR

Links:

UniProtKB: Q13635#VAR_032952; OMIM: 601309.0011; dbSNP: rs199476091

NCBI 1000 Genomes Browser:

rs199476091

Molecular consequence:

NM_000264.5:c.1177G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001083602.3:c.979G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001083603.3:c.1174G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001083604.3:c.724G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001083605.3:c.724G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001083606.3:c.724G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001083607.3:c.724G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001354918.2:c.1177G>A - missense variant - [Sequence Ontology: SO:0001583]
NR_149061.2:n.2082G>A - 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
SCV000622899	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Benign (Jan 25, 2024)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]
SCV001329324	Illumina Laboratory Services, Illumina	criteria provided, single submitter (ICSL Variant Classification Criteria 13 December 2019)	Benign (Apr 27, 2017)	germline	clinical testing	Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000622899

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Benign
(Jan 25, 2024)

germline

clinical testing

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

SCV001329324

Illumina Laboratory Services, Illumina

criteria provided, single submitter

(ICSL Variant Classification Criteria 13 December 2019)

Benign
(Apr 27, 2017)

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

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, SCV000622899.7

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

#	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

From Illumina Laboratory Services, Illumina, SCV001329324.1

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

Description

This variant was observed as part of a predisposition screen in an ostensibly healthy population. A literature search was performed for the gene, cDNA change, and amino acid change (where applicable). No publications were found based on this search. Allele frequency data from public databases was too high to be consistent with this variant causing disease. Therefore, this variant is classified as benign.

#	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: Nov 3, 2024

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