NM_002769.5(PRSS1):c.390C>T (p.Thr130=) AND Hereditary pancreatitis

Germline classification:: Likely benign (3 submissions)
Last evaluated:: Dec 18, 2023
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:: RCV000149415.21

Allele description [Variation Report for NM_002769.5(PRSS1):c.390C>T (p.Thr130=)]

NM_002769.5(PRSS1):c.390C>T (p.Thr130=)

Genes:

TRB:T cell receptor beta locus [Gene - HGNC]
PRSS1:serine protease 1 [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

7q34

Genomic location:

Preferred name:

NM_002769.5(PRSS1):c.390C>T (p.Thr130=)

HGVS:

NC_000007.14:g.142751963C>T
NG_001333.2:g.585631C>T
NG_008307.3:g.7480C>T
NM_002769.5:c.390C>TMANE SELECT
NP_002760.1:p.Thr130=
LRG_1013t1:c.390C>T
LRG_1013:g.7480C>T
LRG_1013p1:p.Thr130=
NC_000007.13:g.142459814C>T
NM_002769.4:c.390C>T
p.Thr130Thr

Links:

dbSNP: rs561097415

NCBI 1000 Genomes Browser:

rs561097415

Molecular consequence:

NM_002769.5:c.390C>T - synonymous variant - [Sequence Ontology: SO:0001819]

Condition(s)

Name:: Hereditary pancreatitis (PCTT)
Synonyms:: Hereditary chronic pancreatitis
Identifiers:: MONDO: MONDO:0008185; MedGen: C0238339; Orphanet: 676; OMIM: 167800

Recent activity

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PREDICTED: Xiphophorus couchianus epithelial membrane protein 3-like (LOC1141415...
PREDICTED: Xiphophorus couchianus epithelial membrane protein 3-like (LOC114141538), transcript variant X3, mRNA
gi|1570429713|ref|XM_028012130.1|

Nucleotide
Bovine viral diarrhea virus partial 5'UTR region, genotype BVDV1a, strain MRI280...
Bovine viral diarrhea virus partial 5'UTR region, genotype BVDV1a, strain MRI2805
gi|1220256907|emb|LT902912.1|

Nucleotide
Bovine viral diarrhea virus partial 5'UTR region, genotype BVDV1b, strain MRI281...
Bovine viral diarrhea virus partial 5'UTR region, genotype BVDV1b, strain MRI2816
gi|1220256915|emb|LT902920.1|

Nucleotide
Bovine viral diarrhea virus partial 5'UTR region, genotype BVDV1a, strain MRI283...
Bovine viral diarrhea virus partial 5'UTR region, genotype BVDV1a, strain MRI2839
gi|1220256934|emb|LT902939.1|

Nucleotide
Bovine viral diarrhea virus partial 5'UTR region, genotype BVDV1a, strain MRI286...
Bovine viral diarrhea virus partial 5'UTR region, genotype BVDV1a, strain MRI2868
gi|1220256955|emb|LT902960.1|

Nucleotide

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000196056	Forschungslabor Klinik Innere Medizin A University Medicine Greifswald	no assertion criteria provided	unknown	inherited	not provided
SCV000630746	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Likely benign (Dec 18, 2023)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]
SCV001183031	Ambry Genetics	criteria provided, single submitter (Ambry Variant Classification Scheme 2023)	Likely benign (Sep 21, 2018)	germline	clinical testing	Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000196056

Forschungslabor Klinik Innere Medizin A University Medicine Greifswald

no assertion criteria provided

unknown

inherited

not provided

SCV000630746

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Likely benign
(Dec 18, 2023)

germline

clinical testing

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

SCV001183031

Ambry Genetics

criteria provided, single submitter

(Ambry Variant Classification Scheme 2023)

Likely benign
(Sep 21, 2018)

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
not provided	inherited	not provided	not provided	not provided	not provided	2	not provided	literature only

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 Forschungslabor Klinik Innere Medizin A University Medicine Greifswald, SCV000196056.1

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

Description

Converted during submission to Uncertain significance.

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	inherited	not provided	2	not provided	not provided		not provided	not provided	not provided	not provided

From Labcorp Genetics (formerly Invitae), Labcorp, SCV000630746.6

#	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 Ambry Genetics, SCV001183031.4

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

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.

#	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: Oct 20, 2024

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