NM_181882.3(PRX):c.3186G>T (p.Lys1062Asn) AND not provided

Germline classification:: Uncertain significance (4 submissions)
Last evaluated:: Aug 12, 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:: RCV000766571.33

Allele description [Variation Report for NM_181882.3(PRX):c.3186G>T (p.Lys1062Asn)]

NM_181882.3(PRX):c.3186G>T (p.Lys1062Asn)

Gene:

PRX:periaxin [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

19q13.2

Genomic location:

Preferred name:

NM_181882.3(PRX):c.3186G>T (p.Lys1062Asn)

HGVS:

NC_000019.10:g.40395166C>A
NG_007979.1:g.23199G>T
NG_051224.1:g.56G>T
NM_020956.2:c.*3391G>T
NM_181882.3:c.3186G>TMANE SELECT
NP_870998.2:p.Lys1062Asn
NP_870998.2:p.Lys1062Asn
LRG_265t1:c.*3391G>T
LRG_265t2:c.3186G>T
LRG_265:g.23199G>T
LRG_265p2:p.Lys1062Asn
NC_000019.9:g.40901073C>A
NM_181882.2:c.3186G>T
NM_181882.3:c.3186G>T

Protein change:

K1062N

Links:

dbSNP: rs139188673

NCBI 1000 Genomes Browser:

rs139188673

Molecular consequence:

NM_020956.2:c.*3391G>T - 3 prime UTR variant - [Sequence Ontology: SO:0001624]
NM_181882.3:c.3186G>T - missense variant - [Sequence Ontology: SO:0001583]

Observations:

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
SCV000293108	GeneDx	criteria provided, single submitter (GeneDx Variant Classification Process June 2021)	Uncertain significance (Aug 12, 2024)	germline	clinical testing	Citation Link,
SCV001715529	Mayo Clinic Laboratories, Mayo Clinic	criteria provided, single submitter (ACMG Guidelines, 2015)	Uncertain significance (Apr 3, 2023)	germline	clinical testing	PubMed (7) [See all records that cite these PMIDs] 2758284, 31523542, 32085570, 32376792, 32453099, 35509735, 25741868
SCV002063770	CeGaT Center for Human Genetics Tuebingen	criteria provided, single submitter (CeGaT Center For Human Genetics Tuebingen Variant Classification Criteria Version 2)	Uncertain significance (Dec 1, 2021)	germline	clinical testing	Citation Link,
SCV004564879	ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories	criteria provided, single submitter (ARUP Molecular Germline Variant Investigation Process 2024)	Uncertain significance (Oct 26, 2023)	germline	clinical testing	Citation Link

Help

Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	germline	yes	1	not provided	not provided	not provided	not provided	clinical testing
not provided	germline	unknown	10	not provided	not provided	not provided	not provided	clinical testing

Citations

PubMed

Treatment of cancer of the colon.

Ramesh H, Thomas PG.

Br J Surg. 1989 Jun;76(6):654. No abstract available.

PubMed [citation]

PMID:: 2758284

A Case Report on Charcot-Marie-Tooth Disease with a Novel Periaxin Gene Mutation.

Datta S, Kataria S, Govindarajan R.

Cureus. 2019 Jul 9;11(7):e5111. doi: 10.7759/cureus.5111.

PubMed [citation]

PMID:: 31523542
PMCID:: PMC6741374

See all PubMed Citations (7)

Details of each submission

From GeneDx, SCV000293108.12

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

Description

Identified in the heterozygous state in an individual with a mild clinical form of CMT4F (PMID: 31523542); Identified in an individual receiving paclitaxel treatment who was reported to have low or no neuropathy (PMID: 27582484); In silico analysis supports that this missense variant has a deleterious effect on protein structure/function; This variant is associated with the following publications: (PMID: 32085570, 32376792, 35509735, 37091313, 27582484, 31523542)

#	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 Mayo Clinic Laboratories, Mayo Clinic, SCV001715529.2

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	10	not provided	not provided	clinical testing	PubMed (7)

Description

BP4

#	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		10	not provided	not provided	not provided

From CeGaT Center for Human Genetics Tuebingen, SCV002063770.20

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

From ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories, SCV004564879.1

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

Description

The PRX c.3186G>T; p.Lys1062Asn variant (rs139188673) is reported in the literature in multiple individuals with suspected CMT (Datta 2019, Volodarsky 2021). This variant is also reported in ClinVar (Variation ID: 245910). This variant is found in the non-Finnish European population with an allele frequency of 0.16% (204/129,096 alleles) in the Genome Aggregation Database. Computational analyses predict that this variant is neutral (REVEL: 0.101). While the high population frequency suggests that this is likely a benign variant, given the lack of clinical and functional data, the significance of this variant is uncertain at this time. References: Datta S et al. A Case Report on Charcot-Marie-Tooth Disease with a Novel Periaxin Gene Mutation. Cureus. 2019 Jul 9;11(7):e5111. PMID: 31523542. Volodarsky M et al. Comprehensive genetic sequence and copy number analysis for Charcot-Marie-Tooth disease in a Canadian cohort of 2517 patients. J Med Genet. 2021 Apr;58(4):284-288. PMID: 32376792.

#	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: Oct 20, 2024

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