NC_000005.10:g.(?_147824661)_(147831792_?)del AND Hereditary pancreatitis

This record was updated by the submitter. Please see the current version.

Germline classification:: Pathogenic (1 submission)
Last evaluated:: Jan 11, 2022
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:: RCV001031457.4

Allele description

NC_000005.10:g.(?_147824661)_(147831792_?)del

Gene:

SPINK1:serine peptidase inhibitor Kazal type 1 [Gene - OMIM - HGNC]

Variant type:

Deletion

Cytogenetic location:

5q32

Genomic location:

Chr5: 147204224 - 147211355 (on Assembly GRCh37)

Preferred name:

NC_000005.10:g.(?_147824661)_(147831792_?)del

HGVS:

NC_000005.10:g.(?_147824661)_(147831792_?)del
NC_000005.9:g.(?_147204224)_(147211355_?)del

Condition(s)

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

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV001194763	Invitae	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Pathogenic (Jan 11, 2022)	germline	clinical testing	PubMed (3) [See all records that cite these PMIDs] 22572128, 17681820, 28492532

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV001194763

Invitae

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Pathogenic
(Jan 11, 2022)

germline

clinical testing

PubMed (3)
[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

Whole exome sequencing identifies multiple, complex etiologies in an idiopathic hereditary pancreatitis kindred.

LaRusch J, Barmada MM, Solomon S, Whitcomb DC.

JOP. 2012 May 10;13(3):258-62.

PubMed [citation]

PMID:: 22572128
PMCID:: PMC3651649

Co-inheritance of a novel deletion of the entire SPINK1 gene with a CFTR missense mutation (L997F) in a family with chronic pancreatitis.

Masson E, Le Maréchal C, Levy P, Chuzhanova N, Ruszniewski P, Cooper DN, Chen JM, Férec C.

Mol Genet Metab. 2007 Sep-Oct;92(1-2):168-75. Epub 2007 Jul 27.

PubMed [citation]

PMID:: 17681820

See all PubMed Citations (3)

Details of each submission

From Invitae, SCV001194763.3

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (3)

Description

A gross deletion of the genomic region encompassing the full coding sequence of the SPINK1 gene has been identified. Loss-of-function variants in SPINK1 are known to be pathogenic (PMID: 17681820, 22572128). The boundaries of this event are unknown as they extend beyond the assayed region for this gene and therefore may encompass additional genes. A similar copy number variant has been observed in individual(s) with chronic pancreatitis (PMID: 17681820). 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: Feb 18, 2023

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