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NM_001386393.1(PANK2):c.370A>G (p.Thr124Ala) AND not specified

Germline classification:
Uncertain significance (1 submission)
Last evaluated:
May 9, 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:
RCV003234892.1

Allele description [Variation Report for NM_001386393.1(PANK2):c.370A>G (p.Thr124Ala)]

NM_001386393.1(PANK2):c.370A>G (p.Thr124Ala)

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.370A>G (p.Thr124Ala)
Other names:
T124A
HGVS:
  • NC_000020.11:g.3907997A>G
  • NG_008131.3:g.24159A>G
  • NM_001324191.2:c.-174A>G
  • NM_001324192.1:c.700A>G
  • NM_001324193.2:c.-466A>G
  • NM_001386393.1:c.370A>GMANE SELECT
  • NM_024960.6:c.-174A>G
  • NM_153638.3:c.700A>G
  • NM_153638.4:c.700A>G
  • NM_153640.4:c.-174A>G
  • NP_001311121.1:p.Thr234Ala
  • NP_001373322.1:p.Thr124Ala
  • NP_705902.2:p.Thr234Ala
  • LRG_1016t1:c.700A>G
  • LRG_1016t2:c.370A>G
  • LRG_1016:g.24159A>G
  • LRG_1016p1:p.Thr234Ala
  • LRG_1016p2:p.Thr124Ala
  • NC_000020.10:g.3888644A>G
  • NR_136715.2:n.414A>G
  • Q9BZ23:p.Thr234Ala
Protein change:
T234A; THR124ALA
Links:
UniProtKB: Q9BZ23#VAR_015155; OMIM: 606157.0008; dbSNP: rs137852965
NCBI 1000 Genomes Browser:
rs137852965
Molecular consequence:
  • NM_001324191.2:c.-174A>G - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
  • NM_001324193.2:c.-466A>G - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
  • NM_024960.6:c.-174A>G - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
  • NM_153640.4:c.-174A>G - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
  • NM_001324192.1:c.700A>G - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001386393.1:c.370A>G - missense variant - [Sequence Ontology: SO:0001583]
  • NM_153638.4:c.700A>G - missense variant - [Sequence Ontology: SO:0001583]
  • NR_136715.2:n.414A>G - non-coding transcript variant - [Sequence Ontology: SO:0001619]

Condition(s)

Synonyms:
AllHighlyPenetrant
Identifiers:
MedGen: CN169374

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV003934223Women's Health and Genetics/Laboratory Corporation of America, LabCorp
criteria provided, single submitter

(LabCorp Variant Classification Summary - May 2015)		Uncertain significance
(May 9, 2023) 		germlineclinical testing

PubMed (10)
[See all records that cite these PMIDs]

Citation Link

Help

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineunknownnot providednot providednot providednot providednot providedclinical 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 (10)

Details of each submission

From Women's Health and Genetics/Laboratory Corporation of America, LabCorp, SCV003934223.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (10)

Description

Variant summary: PANK2 c.700A>G (p.Thr234Ala) results in a non-conservative amino acid change in the encoded protein sequence. Four of five in-silico tools predict a damaging effect of the variant on protein function. The variant allele was found at a frequency of 1.6e-05 in 251292 control chromosomes. c.700A>G has been reported in the literature as a biallelic compound heterozygous genotyp in individuals affected with Pantothenate Kinase-Associated Neurodegeneration (example, Zhou_2001, cited in Hayflick_2003 and Thomas_2004; Egan_2005). These data indicate that the variant may be associated with disease. At least one publication reports experimental evidence evaluating an impact on protein function (Kotzbauer_2005). These results showed no damaging effect of this variant. The following publications have been ascertained in the context of this evaluation (PMID: 28113101, 16023068, 12510040, 15659606, 16450344, 27544236, 14743358, 26547561, 16272150, 11479594). One clinical diagnostic laboratory has submitted clinical-significance assessments for this variant to ClinVar after 2014 and classified the variant as uncertain significance. Based on the evidence outlined above, the variant was classified as VUS-possibly pathogenic.

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknownnot providednot providednot providednot providednot providednot providednot provided

Last Updated: Oct 20, 2024