NM_001386393.1(PANK2):c.67A>G (p.Met23Val) AND Pigmentary pallidal degeneration

Germline classification:: Pathogenic (1 submission)
Last evaluated:: May 13, 2021
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:: RCV001420152.2

Allele description [Variation Report for NM_001386393.1(PANK2):c.67A>G (p.Met23Val)]

NM_001386393.1(PANK2):c.67A>G (p.Met23Val)

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.67A>G (p.Met23Val)

HGVS:

NC_000020.11:g.3889497A>G
NG_008131.3:g.5659A>G
NM_001324191.2:c.-645A>G
NM_001324192.1:c.397A>G
NM_001386393.1:c.67A>GMANE SELECT
NM_024960.6:c.-246+593A>G
NM_153638.4:c.397A>G
NP_001311121.1:p.Met133Val
NP_001373322.1:p.Met23Val
NP_705902.2:p.Met133Val
LRG_1016t1:c.397A>G
LRG_1016t2:c.67A>G
LRG_1016:g.5659A>G
LRG_1016p1:p.Met133Val
LRG_1016p2:p.Met23Val
NC_000020.10:g.3870144A>G
NM_153638.3:c.397A>G
NR_136715.2:n.111A>G

Protein change:

M133V

Links:

dbSNP: rs2146804825

NCBI 1000 Genomes Browser:

rs2146804825

Molecular consequence:

NM_001324191.2:c.-645A>G - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_024960.6:c.-246+593A>G - intron variant - [Sequence Ontology: SO:0001627]
NM_001324192.1:c.397A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001386393.1:c.67A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_153638.4:c.397A>G - missense variant - [Sequence Ontology: SO:0001583]
NR_136715.2:n.111A>G - 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

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV001622416	Genetics and Prenatal Diagnosis Center, The First Affiliated Hospital of Zhengzhou University	criteria provided, single submitter (ACMG Guidelines, 2015)	Pathogenic (May 13, 2021)	germline	clinical testing	PubMed (2) [See all records that cite these PMIDs] 25741868, 28881514

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV001622416

Genetics and Prenatal Diagnosis Center, The First Affiliated Hospital of Zhengzhou University

criteria provided, single submitter

(ACMG Guidelines, 2015)

Pathogenic
(May 13, 2021)

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	yes	not provided	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

[Phenotypic and genotypic features of twenty children with classic pantothenate kinase-associated neurodegeneration].

Zhou J, He J, Kou LP, Feng HC, Deng YH, Zhang ZB, Zhou L, Wang JM, Jiang YW, Wu Y.

Zhonghua Er Ke Za Zhi. 2017 Sep 2;55(9):678-682. doi: 10.3760/cma.j.issn.0578-1310.2017.09.011. Chinese.

PubMed [citation]

PMID:: 28881514

Details of each submission

From Genetics and Prenatal Diagnosis Center, The First Affiliated Hospital of Zhengzhou University, SCV001622416.1

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

#	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: Jul 7, 2024

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