NM_000492.4(CFTR):c.1392G>T (p.Lys464Asn) AND Hereditary pancreatitis

Germline classification:: Pathogenic/Likely pathogenic (2 submissions)
Last evaluated:: Jun 11, 2021
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:: RCV001197496.4

Allele description [Variation Report for NM_000492.4(CFTR):c.1392G>T (p.Lys464Asn)]

NM_000492.4(CFTR):c.1392G>T (p.Lys464Asn)

Genes:

CFTR:CF transmembrane conductance regulator [Gene - OMIM - HGNC]
CFTR-AS1:CFTR antisense RNA 1 [Gene - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

7q31.2

Genomic location:

Preferred name:

NM_000492.4(CFTR):c.1392G>T (p.Lys464Asn)

HGVS:

NC_000007.14:g.117548823G>T
NG_016465.4:g.88040G>T
NM_000492.4:c.1392G>TMANE SELECT
NP_000483.3:p.Lys464Asn
NP_000483.3:p.Lys464Asn
LRG_663t1:c.1392G>T
LRG_663:g.88040G>T
LRG_663p1:p.Lys464Asn
NC_000007.13:g.117188877G>T
NM_000492.3:c.1392G>T

Protein change:

K464N

Links:

dbSNP: rs397508198

NCBI 1000 Genomes Browser:

rs397508198

Molecular consequence:

NM_000492.4:c.1392G>T - missense variant - [Sequence Ontology: SO:0001583]

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
SCV001368262	Centre for Mendelian Genomics, University Medical Centre Ljubljana	criteria provided, single submitter (ACMG Guidelines, 2015)	Pathogenic (Oct 3, 2019)	unknown	clinical testing	PubMed (1) [See all records that cite this PMID]
SCV002529675	Sema4, Sema4	criteria provided, single submitter (Sema4 Curation Guidelines)	Likely pathogenic (Jun 11, 2021)	germline	curation	PubMed (5) [See all records that cite these PMIDs] 23261175, 25403292, 28603918, 28736296, 28784578 Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV001368262

Centre for Mendelian Genomics, University Medical Centre Ljubljana

criteria provided, single submitter

(ACMG Guidelines, 2015)

Pathogenic
(Oct 3, 2019)

unknown

clinical testing

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

SCV002529675

Sema4, Sema4

criteria provided, single submitter

(Sema4 Curation Guidelines)

Likely pathogenic
(Jun 11, 2021)

germline

curation

PubMed (5)
[See all records that cite these PMIDs]

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	curation
not provided	unknown	yes	not provided	not provided	not provided	not provided	not provided	clinical testing

Citations

PubMed

Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology.

Richards S, Aziz N, Bale S, Bick D, Das S, Gastier-Foster J, Grody WW, Hegde M, Lyon E, Spector E, Voelkerding K, Rehm HL; ACMG Laboratory Quality Assurance Committee..

Genet Med. 2015 May;17(5):405-24. doi: 10.1038/gim.2015.30. Epub 2015 Mar 5.

PubMed [citation]

PMID:: 25741868
PMCID:: PMC4544753

Consequences of partial duplications of the human CFTR gene on cf diagnosis: mutations or ectopic variations.

El-Seedy A, Pasquet MC, Bienvenu T, Bieth E, Audrezet MP, Kitzis A, Ladeveze V.

J Cyst Fibros. 2013 Jul;12(4):407-10. doi: 10.1016/j.jcf.2012.11.006. Epub 2012 Dec 21.

PubMed [citation]

PMID:: 23261175

See all PubMed Citations (6)

Details of each submission

From Centre for Mendelian Genomics, University Medical Centre Ljubljana, SCV001368262.2

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

Description

This variant was classified as: Pathogenic. The following ACMG criteria were applied in classifying this variant: PS1,PS3,PM2,PP3.

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

From Sema4, Sema4, SCV002529675.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	curation	PubMed (5)

#	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: May 7, 2024

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