NM_015158.5(KANK1):c.3996G>A (p.Pro1332=) AND not provided

Germline classification:: Uncertain significance (3 submissions)
Last evaluated:: Jul 17, 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:: RCV001730292.7

Allele description [Variation Report for NM_015158.5(KANK1):c.3996G>A (p.Pro1332=)]

NM_015158.5(KANK1):c.3996G>A (p.Pro1332=)

Gene:

KANK1:KN motif and ankyrin repeat domains 1 [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

9p24.3

Genomic location:

Preferred name:

NM_015158.5(KANK1):c.3996G>A (p.Pro1332=)

HGVS:

NC_000009.12:g.744589G>A
NG_016331.2:g.279296G>A
NM_001256876.3:c.3996G>A
NM_001256877.3:c.3996G>A
NM_001354331.2:c.3756G>A
NM_001354332.2:c.3942G>A
NM_001354333.2:c.3522G>A
NM_001354334.2:c.3996G>A
NM_001354335.2:c.3522G>A
NM_001354336.2:c.3228G>A
NM_001354337.2:c.3522G>A
NM_001354338.2:c.3468G>A
NM_001354339.2:c.3282G>A
NM_001354340.2:c.3468G>A
NM_001354341.2:c.3522G>A
NM_001354342.2:c.3282G>A
NM_001354343.2:c.3282G>A
NM_001354344.2:c.3468G>A
NM_015158.5:c.3996G>AMANE SELECT
NM_153186.6:c.3522G>A
NP_001243805.1:p.Pro1332=
NP_001243806.1:p.Pro1332=
NP_001341260.1:p.Pro1252=
NP_001341261.1:p.Pro1314=
NP_001341262.1:p.Pro1174=
NP_001341263.1:p.Pro1332=
NP_001341264.1:p.Pro1174=
NP_001341265.1:p.Pro1076=
NP_001341266.1:p.Pro1174=
NP_001341267.1:p.Pro1156=
NP_001341268.1:p.Pro1094=
NP_001341269.1:p.Pro1156=
NP_001341270.1:p.Pro1174=
NP_001341271.1:p.Pro1094=
NP_001341272.1:p.Pro1094=
NP_001341273.1:p.Pro1156=
NP_055973.2:p.Pro1332=
NP_694856.1:p.Pro1174=
NC_000009.11:g.744589G>A
NM_015158.2:c.3996G>A
NR_148869.2:n.4124G>A

Links:

dbSNP: rs115382946

NCBI 1000 Genomes Browser:

rs115382946

Molecular consequence:

NR_148869.2:n.4124G>A - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NM_001256876.3:c.3996G>A - synonymous variant - [Sequence Ontology: SO:0001819]
NM_001256877.3:c.3996G>A - synonymous variant - [Sequence Ontology: SO:0001819]
NM_001354331.2:c.3756G>A - synonymous variant - [Sequence Ontology: SO:0001819]
NM_001354332.2:c.3942G>A - synonymous variant - [Sequence Ontology: SO:0001819]
NM_001354333.2:c.3522G>A - synonymous variant - [Sequence Ontology: SO:0001819]
NM_001354334.2:c.3996G>A - synonymous variant - [Sequence Ontology: SO:0001819]
NM_001354335.2:c.3522G>A - synonymous variant - [Sequence Ontology: SO:0001819]
NM_001354336.2:c.3228G>A - synonymous variant - [Sequence Ontology: SO:0001819]
NM_001354337.2:c.3522G>A - synonymous variant - [Sequence Ontology: SO:0001819]
NM_001354338.2:c.3468G>A - synonymous variant - [Sequence Ontology: SO:0001819]
NM_001354339.2:c.3282G>A - synonymous variant - [Sequence Ontology: SO:0001819]
NM_001354340.2:c.3468G>A - synonymous variant - [Sequence Ontology: SO:0001819]
NM_001354341.2:c.3522G>A - synonymous variant - [Sequence Ontology: SO:0001819]
NM_001354342.2:c.3282G>A - synonymous variant - [Sequence Ontology: SO:0001819]
NM_001354343.2:c.3282G>A - synonymous variant - [Sequence Ontology: SO:0001819]
NM_001354344.2:c.3468G>A - synonymous variant - [Sequence Ontology: SO:0001819]
NM_015158.5:c.3996G>A - synonymous variant - [Sequence Ontology: SO:0001819]
NM_153186.6:c.3522G>A - synonymous variant - [Sequence Ontology: SO:0001819]

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
SCV001978481	Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen - VKGL Data-share Consensus	no assertion criteria provided	Uncertain significance	germline	clinical testing
SCV001980585	Clinical Genetics DNA and cytogenetics Diagnostics Lab, Erasmus MC, Erasmus Medical Center - VKGL Data-share Consensus See additional submitters Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen	no assertion criteria provided	Uncertain significance	germline	clinical testing
SCV002225801	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (Jul 17, 2023)	germline	clinical testing	PubMed (3) [See all records that cite these PMIDs] 17576681, 9536098, 28492532

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV001978481

Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen - VKGL Data-share Consensus

no assertion criteria provided

Uncertain significance

germline

clinical testing

SCV001980585

Clinical Genetics DNA and cytogenetics Diagnostics Lab, Erasmus MC, Erasmus Medical Center - VKGL Data-share Consensus

See additional submitters

no assertion criteria provided

Uncertain significance

germline

clinical testing

SCV002225801

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(Jul 17, 2023)

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	yes	not provided	not provided	not provided	not provided	not provided	clinical testing
not provided	germline	unknown	not provided	not provided	not provided	not provided	not provided	clinical testing

Citations

PubMed

Aberrant 5' splice sites in human disease genes: mutation pattern, nucleotide structure and comparison of computational tools that predict their utilization.

Buratti E, Chivers M, Královicová J, Romano M, Baralle M, Krainer AR, Vorechovsky I.

Nucleic Acids Res. 2007;35(13):4250-63. Epub 2007 Jun 18.

PubMed [citation]

PMID:: 17576681
PMCID:: PMC1934990

Statistical features of human exons and their flanking regions.

Zhang MQ.

Hum Mol Genet. 1998 May;7(5):919-32.

PubMed [citation]

PMID:: 9536098

See all PubMed Citations (3)

Details of each submission

From Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen - VKGL Data-share Consensus, SCV001978481.1

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

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

From Clinical Genetics DNA and cytogenetics Diagnostics Lab, Erasmus MC, Erasmus Medical Center - VKGL Data-share Consensus, SCV001980585.1

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

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

From Labcorp Genetics (formerly Invitae), Labcorp, SCV002225801.3

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

Description

This sequence change affects codon 1332 of the KANK1 mRNA. It is a 'silent' change, meaning that it does not change the encoded amino acid sequence of the KANK1 protein. This variant also falls at the last nucleotide of exon 11, which is part of the consensus splice site for this exon. This variant is present in population databases (rs115382946, gnomAD 0.03%). This variant has not been reported in the literature in individuals affected with KANK1-related conditions. ClinVar contains an entry for this variant (Variation ID: 1299864). Variants that disrupt the consensus splice site are a relatively common cause of aberrant splicing (PMID: 17576681, 9536098). Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant may disrupt the consensus splice site. In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance.

#	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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