NM_001386393.1(PANK2):c.1090_1096del (p.Gly363_Asn364insTer) AND Pigmentary pallidal degeneration

Germline classification:: Pathogenic (1 submission)
Last evaluated:: Jun 14, 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:: RCV003503001.2

Allele description [Variation Report for NM_001386393.1(PANK2):c.1090_1096del (p.Gly363_Asn364insTer)]

NM_001386393.1(PANK2):c.1090_1096del (p.Gly363_Asn364insTer)

Gene:

PANK2:pantothenate kinase 2 [Gene - OMIM - HGNC]

Variant type:

Deletion

Cytogenetic location:

20p13

Genomic location:

Preferred name:

NM_001386393.1(PANK2):c.1090_1096del (p.Gly363_Asn364insTer)

HGVS:

NC_000020.11:g.3916934_3916940del
NG_008131.3:g.33096_33102del
NM_001324191.2:c.547_553del
NM_001324193.2:c.112_118del
NM_001386393.1:c.1090_1096delMANE SELECT
NM_024960.6:c.547_553del
NM_153638.4:c.1420_1426del
NM_153640.4:c.547_553del
NP_001311120.1:p.Gly182_Asn183insTer
NP_001311122.1:p.Gly37_Asn38insTer
NP_001373322.1:p.Gly363_Asn364insTer
NP_079236.3:p.Gly182_Asn183insTer
NP_705902.2:p.Gly473_Asn474insTer
NP_705904.1:p.Gly182_Asn183insTer
LRG_1016t1:c.1420_1426del
LRG_1016t2:c.1090_1096del
LRG_1016:g.33096_33102del
LRG_1016p1:p.Gly473_Asn474insTer
LRG_1016p2:p.Gly363_Asn364insTer
NC_000020.10:g.3897579_3897585del
NC_000020.10:g.3897581_3897587del
NR_136715.2:n.991_997del

Molecular consequence:

NR_136715.2:n.991_997del - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NM_001324191.2:c.547_553del - nonsense - [Sequence Ontology: SO:0001587]
NM_001324193.2:c.112_118del - nonsense - [Sequence Ontology: SO:0001587]
NM_001386393.1:c.1090_1096del - nonsense - [Sequence Ontology: SO:0001587]
NM_024960.6:c.547_553del - nonsense - [Sequence Ontology: SO:0001587]
NM_153638.4:c.1420_1426del - nonsense - [Sequence Ontology: SO:0001587]
NM_153640.4:c.547_553del - nonsense - [Sequence Ontology: SO:0001587]

Condition(s)

Name:: Pigmentary pallidal degeneration (NBIA1)
Synonyms:: PKAN NEUROAXONAL DYSTROPHY, JUVENILE-ONSET; Pantothenate kinase-associated neurodegeneration; Neuroaxonal dystrophy, late infantile; See all synonyms [MedGen]
Identifiers:: MONDO: MONDO:0009319; MedGen: C0018523; Orphanet: 157850; OMIM: 234200

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV004318418	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Pathogenic (Jun 14, 2023)	germline	clinical testing	PubMed (2) [See all records that cite these PMIDs] 16437574, 28492532

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV004318418

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Pathogenic
(Jun 14, 2023)

germline

clinical testing

PubMed (2)
[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

Genotypic and phenotypic spectrum of PANK2 mutations in patients with neurodegeneration with brain iron accumulation.

Hartig MB, Hörtnagel K, Garavaglia B, Zorzi G, Kmiec T, Klopstock T, Rostasy K, Svetel M, Kostic VS, Schuelke M, Botz E, Weindl A, Novakovic I, Nardocci N, Prokisch H, Meitinger T.

Ann Neurol. 2006 Feb;59(2):248-56.

PubMed [citation]

PMID:: 16437574

Sherloc: a comprehensive refinement of the ACMG-AMP variant classification criteria.

Nykamp K, Anderson M, Powers M, Garcia J, Herrera B, Ho YY, Kobayashi Y, Patil N, Thusberg J, Westbrook M; Invitae Clinical Genomics Group., Topper S.

Genet Med. 2017 Oct;19(10):1105-1117. doi: 10.1038/gim.2017.37. Epub 2017 May 11. Erratum in: Genet Med. 2020 Jan;22(1):240. doi: 10.1038/s41436-019-0624-9.

PubMed [citation]

PMID:: 28492532
PMCID:: PMC5632818

Details of each submission

From Labcorp Genetics (formerly Invitae), Labcorp, SCV004318418.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (2)

Description

For these reasons, this variant has been classified as Pathogenic. This premature translational stop signal has been observed in individual(s) with neurodegeneration with brain iron accumulation (PMID: 16437574). This variant is not present in population databases (gnomAD no frequency). This sequence change creates a premature translational stop signal (p.Asn474*) in the PANK2 gene. However, it is currently unclear if variants that occur in this region of the gene cause disease.

#	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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