NM_001386393.1(PANK2):c.53G>A (p.Arg18Gln) AND Pigmentary pallidal degeneration

Germline classification:: Conflicting classifications of pathogenicity (2 submissions)
Last evaluated:: Jan 25, 2026
Review status:: criteria provided, conflicting classifications

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:: RCV000631205.15

Allele description [Variation Report for NM_001386393.1(PANK2):c.53G>A (p.Arg18Gln)]

NM_001386393.1(PANK2):c.53G>A (p.Arg18Gln)

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.53G>A (p.Arg18Gln)

HGVS:

NC_000020.11:g.3889483G>A
NG_008131.3:g.5645G>A
NM_001324191.2:c.-659G>A
NM_001324192.1:c.383G>A
NM_001386393.1:c.53G>AMANE SELECT
NM_024960.6:c.-246+579G>A
NM_153638.4:c.383G>A
NP_001311121.1:p.Arg128Gln
NP_001373322.1:p.Arg18Gln
NP_705902.2:p.Arg128Gln
LRG_1016t1:c.383G>A
LRG_1016t2:c.53G>A
LRG_1016:g.5645G>A
LRG_1016p1:p.Arg128Gln
LRG_1016p2:p.Arg18Gln
NC_000020.10:g.3870130G>A
NM_153638.2:c.383G>A
NM_153638.3:c.383G>A
NR_136715.2:n.97G>A

Protein change:

R128Q

Links:

dbSNP: rs546381069

Molecular consequence:

NM_001324191.2:c.-659G>A - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_024960.6:c.-246+579G>A - intron variant - [Sequence Ontology: SO:0001627]
NM_001324192.1:c.383G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001386393.1:c.53G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_153638.4:c.383G>A - missense variant - [Sequence Ontology: SO:0001583]
NR_136715.2:n.97G>A - non-coding transcript variant - [Sequence Ontology: SO:0001619]

Condition(s)

Name:: Pigmentary pallidal degeneration (NBIA1)
Synonyms:: PKAN NEUROAXONAL DYSTROPHY, JUVENILE-ONSET; Neuroaxonal dystrophy, late infantile; Hallervorden-Spatz disease; 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
SCV000752219	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Likely benign (Jan 25, 2026)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]
SCV002553238	Department of Neurology, Xijing Hospital, Fourth Military Medical University	criteria provided, single submitter (ACMG Guidelines, 2015)	Uncertain significance (Mar 1, 2022)	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

SCV000752219

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Likely benign
(Jan 25, 2026)

germline

clinical testing

PubMed (1)
[See all records that cite this PMID]

SCV002553238

Department of Neurology, Xijing Hospital, Fourth Military Medical University

criteria provided, single submitter

(ACMG Guidelines, 2015)

Uncertain significance
(Mar 1, 2022)

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

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

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 Labcorp Genetics (formerly Invitae), Labcorp, SCV000752219.9

#	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

From Department of Neurology, Xijing Hospital, Fourth Military Medical University, SCV002553238.1

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

Last Updated: Apr 12, 2026

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