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NM_001379610.1(SPINK1):c.194+2T>C AND SPINK1-related disorder

Germline classification:
Pathogenic (1 submission)
Last evaluated:
May 20, 2024
Review status:
(0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided
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:
RCV003398721.5

Allele description [Variation Report for NM_001379610.1(SPINK1):c.194+2T>C]

NM_001379610.1(SPINK1):c.194+2T>C

Gene:
SPINK1:serine peptidase inhibitor Kazal type 1 [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
5q32
Genomic location:
Preferred name:
NM_001379610.1(SPINK1):c.194+2T>C
Other names:
IVS3+2T>C
HGVS:
  • NC_000005.10:g.147828020A>G
  • NG_008356.2:g.16212T>C
  • NM_001354966.2:c.194+2T>C
  • NM_001379610.1:c.194+2T>CMANE SELECT
  • NM_003122.5:c.194+2T>C
  • NC_000005.9:g.147207583A>G
  • NM_003122.3:c.194+2T>C
  • NM_003122.4:c.194+2T>C
Links:
dbSNP: rs148954387
NCBI 1000 Genomes Browser:
rs148954387
Molecular consequence:
  • NM_001354966.2:c.194+2T>C - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001379610.1:c.194+2T>C - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_003122.5:c.194+2T>C - splice donor variant - [Sequence Ontology: SO:0001575]

Condition(s)

Name:
SPINK1-related disorder
Synonyms:
SPINK1-related condition
Identifiers:

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV004121291PreventionGenetics, part of Exact Sciences
no assertion criteria provided
Pathogenic
(May 20, 2024) 		germlineclinical testing

Help

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineunknownnot providednot providednot providednot providednot providedclinical testing

Details of each submission

From PreventionGenetics, part of Exact Sciences, SCV004121291.2

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testingnot provided

Description

The SPINK1 c.194+2T>C variant is predicted to disrupt the GT donor site and interfere with normal splicing. This variant has been reported as causative for SPINK1-related disorders, including chronic pancreatitis, and functional studies support its pathogenicity (Witt et al. 2000. PubMed ID: 10835640; Kereszturi et al. 2008. PubMed ID: 18978175; Sun et al. 2015. PubMed ID: 26632706). This variant is reported in 0.33% of alleles in individuals of East Asian descent in gnomAD. Variants that disrupt a consensus splice donor site in SPINK1 are expected to be pathogenic. This variant is interpreted as pathogenic.

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

Last Updated: Nov 10, 2024