NM_001386393.1(PANK2):c.189C>G (p.Pro63=) AND not provided

Germline classification:: Likely benign (3 submissions)
Last evaluated:: Oct 15, 2020
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:: RCV000676174.11

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)

Synonyms:: none provided
Identifiers:: MedGen: C3661900

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000801926	Mayo Clinic Laboratories, Mayo Clinic	no assertion criteria provided	Benign (Mar 16, 2016)	unknown	clinical testing
SCV001793400	GeneDx	criteria provided, single submitter (GeneDx Variant Classification Process June 2021)	Likely benign (Oct 15, 2020)	germline	clinical testing	Citation Link,
SCV005207267	Breakthrough Genomics, Breakthrough Genomics	criteria provided, single submitter (ACMG Guidelines, 2015)	Likely benign	germline	not provided	PubMed (1) [See all records that cite this PMID]

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000801926

Mayo Clinic Laboratories, Mayo Clinic

no assertion criteria provided

Benign
(Mar 16, 2016)

unknown

clinical testing

SCV001793400

GeneDx

criteria provided, single submitter

(GeneDx Variant Classification Process June 2021)

Likely benign
(Oct 15, 2020)

germline

clinical testing

Citation Link,

SCV005207267

Breakthrough Genomics, Breakthrough Genomics

criteria provided, single submitter

(ACMG Guidelines, 2015)

Likely benign

germline

not provided

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	yes	not provided	not provided	not provided	not provided	not provided	clinical testing, not provided
not provided	unknown	unknown	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

Details of each submission

From Mayo Clinic Laboratories, Mayo Clinic, SCV000801926.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	not provided

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	unknown	unknown	not provided	not provided	not provided		not provided	not provided	not provided	not provided

From GeneDx, SCV001793400.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	not provided

#	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

From Breakthrough Genomics, Breakthrough Genomics, SCV005207267.1

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

#	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: Sep 29, 2024

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