NM_001386393.1(PANK2):c.1086del (p.Phe362fs) AND Pigmentary pallidal degeneration

Germline classification:: Pathogenic (1 submission)
Last evaluated:: Nov 27, 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:: RCV001905178.6

Allele description [Variation Report for NM_001386393.1(PANK2):c.1086del (p.Phe362fs)]

NM_001386393.1(PANK2):c.1086del (p.Phe362fs)

Gene:

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

Variant type:

Deletion

Cytogenetic location:

20p13

Genomic location:

Preferred name:

NM_001386393.1(PANK2):c.1086del (p.Phe362fs)

HGVS:

NC_000020.11:g.3916930del
NG_008131.3:g.33092del
NM_001324191.2:c.543del
NM_001324193.2:c.108del
NM_001386393.1:c.1086delMANE SELECT
NM_024960.6:c.543del
NM_153638.4:c.1416del
NM_153640.4:c.543del
NP_001311120.1:p.Phe181fs
NP_001311122.1:p.Phe36fs
NP_001373322.1:p.Phe362fs
NP_079236.3:p.Phe181fs
NP_705902.2:p.Phe472fs
NP_705904.1:p.Phe181fs
LRG_1016t1:c.1416del
LRG_1016t2:c.1086del
LRG_1016:g.33092del
LRG_1016p1:p.Phe472fs
LRG_1016p2:p.Phe362fs
NC_000020.10:g.3897575del
NC_000020.10:g.3897577del
NR_136715.2:n.987del

Protein change:

F181fs

Links:

dbSNP: rs2146887806

NCBI 1000 Genomes Browser:

rs2146887806

Molecular consequence:

NM_001324191.2:c.543del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001324193.2:c.108del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001386393.1:c.1086del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_024960.6:c.543del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_153638.4:c.1416del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_153640.4:c.543del - frameshift variant - [Sequence Ontology: SO:0001589]
NR_136715.2:n.987del - non-coding transcript variant - [Sequence Ontology: SO:0001619]

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

Recent activity

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S41 family peptidase [Massilia antarctica]
S41 family peptidase [Massilia antarctica]
gi|1937098242|gnl|PRJNA675950|IV454 5|gb|QPI51692.1|

Protein
S41 family peptidase [Alkalihalobacillus sp. LMS39]
S41 family peptidase [Alkalihalobacillus sp. LMS39]
gi|2216429286|gnl|PRJNA813594|MM271 5|gb|UOE93769.1|

Protein
LOC112029646 [Quercus suber]
LOC112029646 [Quercus suber]
Gene ID:112029646

Gene

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV002130281	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Pathogenic (Nov 27, 2023)	germline	clinical testing	PubMed (3) [See all records that cite these PMIDs] 11479594, 12510040, 28492532

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV002130281

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Pathogenic
(Nov 27, 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	unknown	not provided	not provided	not provided	not provided	not provided	clinical testing

Citations

PubMed

A novel pantothenate kinase gene (PANK2) is defective in Hallervorden-Spatz syndrome.

Zhou B, Westaway SK, Levinson B, Johnson MA, Gitschier J, Hayflick SJ.

Nat Genet. 2001 Aug;28(4):345-9.

PubMed [citation]

PMID:: 11479594

Genetic, clinical, and radiographic delineation of Hallervorden-Spatz syndrome.

Hayflick SJ, Westaway SK, Levinson B, Zhou B, Johnson MA, Ching KH, Gitschier J.

N Engl J Med. 2003 Jan 2;348(1):33-40.

PubMed [citation]

PMID:: 12510040

See all PubMed Citations (3)

Details of each submission

From Labcorp Genetics (formerly Invitae), Labcorp, SCV002130281.3

#	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 creates a premature translational stop signal (p.Phe472Leufs*4) in the PANK2 gene. It is expected to result in an absent or disrupted protein product. Loss-of-function variants in PANK2 are known to be pathogenic (PMID: 11479594, 12510040). This variant is not present in population databases (gnomAD no frequency). This variant has not been reported in the literature in individuals affected with PANK2-related conditions. ClinVar contains an entry for this variant (Variation ID: 1363985). For these reasons, this variant has been classified as Pathogenic.

#	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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