NM_007059.4(KPTN):c.714_731dup (p.Gln246_Asp247insMetTrpSerValLeuGln) AND not provided

Germline classification:: Pathogenic/Likely pathogenic (4 submissions)
Last evaluated:: May 3, 2022
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:: RCV000515002.35

Allele description [Variation Report for NM_007059.4(KPTN):c.714_731dup (p.Gln246_Asp247insMetTrpSerValLeuGln)]

NM_007059.4(KPTN):c.714_731dup (p.Gln246_Asp247insMetTrpSerValLeuGln)

Gene:

KPTN:kaptin, actin binding protein [Gene - OMIM - HGNC]

Variant type:

Duplication

Cytogenetic location:

19q13.32

Genomic location:

Preferred name:

NM_007059.4(KPTN):c.714_731dup (p.Gln246_Asp247insMetTrpSerValLeuGln)

HGVS:

NC_000019.10:g.47479922_47479939dup
NG_034097.1:g.9329_9346dup
NM_001291296.2:c.546_563dup
NM_007059.4:c.714_731dupMANE SELECT
NP_001278225.1:p.Gln190_Asp191insMetTrpSerValLeuGln
NP_008990.2:p.Gln246_Asp247insMetTrpSerValLeuGln
NC_000019.9:g.47983175_47983176insACCGACCACATCTGCAGA
NC_000019.9:g.47983179_47983196dup
NM_007059.2:c.714_731dupTCTGCAGATGTGGTCGGT
NM_007059.3:c.714_731dup
NR_111923.2:n.860_877dup

Links:

OMIM: 615620.0002; dbSNP: rs587777148

NCBI 1000 Genomes Browser:

rs587777148

Molecular consequence:

NM_001291296.2:c.546_563dup - inframe_insertion - [Sequence Ontology: SO:0001821]
NM_007059.4:c.714_731dup - inframe_insertion - [Sequence Ontology: SO:0001821]
NR_111923.2:n.860_877dup - non-coding transcript variant - [Sequence Ontology: SO:0001619]

Observations:

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
SCV000611060	Center for Pediatric Genomic Medicine, Children's Mercy Hospital and Clinics	criteria provided, single submitter (ACMG Guidelines, 2015)	Pathogenic (May 4, 2017)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]
SCV000709882	GeneDx	criteria provided, single submitter (GeneDx Variant Classification Process June 2021)	Pathogenic (May 3, 2022)	germline	clinical testing	Citation Link,
SCV001334672	CeGaT Center for Human Genetics Tuebingen	criteria provided, single submitter (CeGaT Center For Human Genetics Tuebingen Variant Classification Criteria Version 2)	Pathogenic (Oct 1, 2021)	germline	clinical testing	Citation Link,
SCV002066295	Genetic Services Laboratory, University of Chicago	criteria provided, single submitter (ACMG Guidelines, 2015)	Likely pathogenic (May 21, 2018)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]

Help

Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	germline	not provided	not provided	not provided	not provided	not provided	not provided	clinical testing
not provided	germline	yes	5	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

Details of each submission

From Center for Pediatric Genomic Medicine, Children's Mercy Hospital and Clinics, SCV000611060.1

#	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	not provided	not provided	not provided	not provided		not provided	0.000739	not provided	not provided

From GeneDx, SCV000709882.4

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

Description

Published functional studies demonstrate a damaging effect resulting in improper localization of the kaptin protein (Baple et al., 2014); In-frame insertion of 6 amino acids in a non-repeat region; This variant is associated with the following publications: (PMID: 31999056, 24239382, 30008475, 32358097)

#	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 CeGaT Center for Human Genetics Tuebingen, SCV001334672.25

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	5	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		5	not provided	not provided	not provided

From Genetic Services Laboratory, University of Chicago, SCV002066295.1

#	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	yes	not provided	not provided	not provided		not provided	not provided	not provided	not provided

Last Updated: Nov 18, 2024

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