NM_002772.3(TMPRSS15):c.2599_2600insGATTAATAGATGAAATTGTC (p.His867fs) AND not provided

Germline classification:: Pathogenic (1 submission)
Last evaluated:: Oct 13, 2023
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:: RCV002606251.3

Allele description [Variation Report for NM_002772.3(TMPRSS15):c.2599_2600insGATTAATAGATGAAATTGTC (p.His867fs)]

NM_002772.3(TMPRSS15):c.2599_2600insGATTAATAGATGAAATTGTC (p.His867fs)

Gene:

TMPRSS15:transmembrane serine protease 15 [Gene - OMIM - HGNC]

Variant type:

Insertion

Cytogenetic location:

21q21.1

Genomic location:

Preferred name:

NM_002772.3(TMPRSS15):c.2599_2600insGATTAATAGATGAAATTGTC (p.His867fs)

HGVS:

NC_000021.9:g.18281110_18281111insCAATTTCATCTATTAATCGA
NG_012207.2:g.184567_184568insGATTAATAGATGAAATTGTC
NM_002772.3:c.2599_2600insGATTAATAGATGAAATTGTCMANE SELECT
NP_002763.3:p.His867fs
NC_000021.8:g.19653425_19653426insGACAATTTCATCTATTAATC
NC_000021.8:g.19653427_19653428insCAATTTCATCTATTAATCGA
NG_012207.1:g.127545_127546insGATTAATAGATGAAATTGTC

Protein change:

H867fs

Molecular consequence:

NM_002772.3:c.2599_2600insGATTAATAGATGAAATTGTC - frameshift variant - [Sequence Ontology: SO:0001589]

Condition(s)

Synonyms:: none provided
Identifiers:: MedGen: C3661900

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV003499063	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Pathogenic (Oct 13, 2023)	germline	clinical testing	PubMed (2) [See all records that cite these PMIDs] 11719902, 28492532

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV003499063

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Pathogenic
(Oct 13, 2023)

germline

clinical testing

PubMed (2)
[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

Mutations in the proenteropeptidase gene are the molecular cause of congenital enteropeptidase deficiency.

Holzinger A, Maier EM, Bück C, Mayerhofer PU, Kappler M, Haworth JC, Moroz SP, Hadorn HB, Sadler JE, Roscher AA.

Am J Hum Genet. 2002 Jan;70(1):20-5. Epub 2001 Nov 21.

PubMed [citation]

PMID:: 11719902
PMCID:: PMC384888

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, SCV003499063.2

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (2)

Description

This sequence change creates a premature translational stop signal (p.His867Argfs*20) in the TMPRSS15 gene. It is expected to result in an absent or disrupted protein product. Loss-of-function variants in TMPRSS15 are known to be pathogenic (PMID: 11719902). This variant is present in population databases (rs763761460, gnomAD 0.005%). This variant has not been reported in the literature in individuals affected with TMPRSS15-related conditions. ClinVar contains an entry for this variant (Variation ID: 2181643). 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

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