NM_001386393.1(PANK2):c.189C>G (p.Pro63=) AND Pigmentary pallidal degeneration

Germline classification:: Benign/Likely benign (2 submissions)
Last evaluated:: Jan 31, 2024
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:: RCV000335556.13

Allele description [Variation Report for NM_001386393.1(PANK2):c.189C>G (p.Pro63=)]

NM_001386393.1(PANK2):c.189C>G (p.Pro63=)

Genes:

LOC130065345:ATAC-STARR-seq lymphoblastoid silent region 12635 [Gene]
PANK2:pantothenate kinase 2 [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

20p13

Genomic location:

Preferred name:

NM_001386393.1(PANK2):c.189C>G (p.Pro63=)

HGVS:

NC_000020.11:g.3889619C>G
NG_008131.3:g.5781C>G
NM_001324191.2:c.-523C>G
NM_001324192.1:c.519C>G
NM_001386393.1:c.189C>GMANE SELECT
NM_024960.6:c.-246+715C>G
NM_153638.4:c.519C>G
NP_001311121.1:p.Pro173=
NP_001373322.1:p.Pro63=
NP_705902.2:p.Pro173=
LRG_1016t1:c.519C>G
LRG_1016t2:c.189C>G
LRG_1016:g.5781C>G
LRG_1016p1:p.Pro173=
LRG_1016p2:p.Pro63=
NC_000020.10:g.3870266C>G
NM_153638.2:c.519C>G
NR_136715.2:n.233C>G

Links:

dbSNP: rs71647829

NCBI 1000 Genomes Browser:

rs71647829

Molecular consequence:

NM_001324191.2:c.-523C>G - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_024960.6:c.-246+715C>G - intron variant - [Sequence Ontology: SO:0001627]
NR_136715.2:n.233C>G - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NM_001324192.1:c.519C>G - synonymous variant - [Sequence Ontology: SO:0001819]
NM_001386393.1:c.189C>G - synonymous variant - [Sequence Ontology: SO:0001819]
NM_153638.4:c.519C>G - synonymous variant - [Sequence Ontology: SO:0001819]

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
SCV000433813	Illumina Laboratory Services, Illumina	criteria provided, single submitter (ICSL Variant Classification Criteria 13 December 2019)	Likely benign (Apr 27, 2017)	germline	clinical testing	PubMed (2) [See all records that cite these PMIDs] 21459825, 15565311 Citation Link,
SCV001020980	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Benign (Jan 31, 2024)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000433813

Illumina Laboratory Services, Illumina

criteria provided, single submitter

(ICSL Variant Classification Criteria 13 December 2019)

Likely benign
(Apr 27, 2017)

germline

clinical testing

PubMed (2)
[See all records that cite these PMIDs]

Citation Link,

SCV001020980

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Benign
(Jan 31, 2024)

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	unknown	not provided	not provided	not provided	not provided	not provided	clinical testing

Citations

PubMed

Novel histopathologic findings in molecularly-confirmed pantothenate kinase-associated neurodegeneration.

Kruer MC, Hiken M, Gregory A, Malandrini A, Clark D, Hogarth P, Grafe M, Hayflick SJ, Woltjer RL.

Brain. 2011 Apr;134(Pt 4):947-58. doi: 10.1093/brain/awr042.

PubMed [citation]

PMID:: 21459825
PMCID:: PMC3105492

MR relaxometry and 1H MR spectroscopy for the determination of iron and metabolite concentrations in PKAN patients.

Hájek M, Adamovicová M, Herynek V, Skoch A, Jírů F, Krepelová A, Dezortová M.

Eur Radiol. 2005 May;15(5):1060-8. Epub 2004 Nov 24.

PubMed [citation]

PMID:: 15565311

See all PubMed Citations (3)

Details of each submission

From Illumina Laboratory Services, Illumina, SCV000433813.3

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

Description

This variant was observed as part of a predisposition screen in an ostensibly healthy population. A literature search was performed for the gene, cDNA change, and amino acid change (where applicable). Publications were found based on this search. The evidence from the literature, in combination with allele frequency data from public databases where available, was sufficient to determine this variant is unlikely to cause disease. Therefore, this variant is classified as likely benign.

#	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

From Labcorp Genetics (formerly Invitae), Labcorp, SCV001020980.6

#	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	unknown	not provided	not provided	not provided		not provided	not provided	not provided	not provided

Last Updated: Sep 29, 2024

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