NM_014855.3(AP5Z1):c.2014G>A (p.Glu672Lys) AND Hereditary spastic paraplegia

Germline classification:: Uncertain significance (2 submissions)
Last evaluated:: Mar 7, 2017
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:: RCV000515984.4

Allele description [Variation Report for NM_014855.3(AP5Z1):c.2014G>A (p.Glu672Lys)]

NM_014855.3(AP5Z1):c.2014G>A (p.Glu672Lys)

Gene:

AP5Z1:adaptor related protein complex 5 subunit zeta 1 [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

7p22.1

Genomic location:

Preferred name:

NM_014855.3(AP5Z1):c.2014G>A (p.Glu672Lys)

HGVS:

NC_000007.14:g.4790748G>A
NG_028111.1:g.20118G>A
NM_001364858.1:c.1546G>A
NM_014855.3:c.2014G>AMANE SELECT
NP_001351787.1:p.Glu516Lys
NP_055670.1:p.Glu672Lys
LRG_1247t1:c.2014G>A
LRG_1247:g.20118G>A
LRG_1247p1:p.Glu672Lys
NC_000007.13:g.4830379G>A
NM_014855.2:c.2014G>A
NR_157345.1:n.2145G>A

Protein change:

E516K

Links:

dbSNP: rs145463842

NCBI 1000 Genomes Browser:

rs145463842

Molecular consequence:

NM_001364858.1:c.1546G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_014855.3:c.2014G>A - missense variant - [Sequence Ontology: SO:0001583]
NR_157345.1:n.2145G>A - non-coding transcript variant - [Sequence Ontology: SO:0001619]

Condition(s)

Name:: Hereditary spastic paraplegia
Synonyms:: Familial spastic paraparesis
Identifiers:: MONDO: MONDO:0019064; MedGen: C0037773; OMIM: PS303350

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000574507	Unit for Genetic & Epidemiological Research on Neurological Disorders, Instituto de Investigação e Inovação em Saúde	criteria provided, single submitter (Morais et al. (Eur J Hum Genet. 2017))	Uncertain significance (Mar 7, 2017)	unknown	research	PubMed (1) [See all records that cite this PMID]
SCV002106171	Genome Diagnostics Laboratory, The Hospital for Sick Children	criteria provided, single submitter (ACMG Guidelines, 2015)	Uncertain significance (Dec 12, 2016)	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

SCV000574507

Unit for Genetic & Epidemiological Research on Neurological Disorders, Instituto de Investigação e Inovação em Saúde

criteria provided, single submitter

(Morais et al. (Eur J Hum Genet. 2017))

Uncertain significance
(Mar 7, 2017)

unknown

research

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

SCV002106171

Genome Diagnostics Laboratory, The Hospital for Sick Children

criteria provided, single submitter

(ACMG Guidelines, 2015)

Uncertain significance
(Dec 12, 2016)

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	yes	not provided	not provided	not provided	not provided	not provided	clinical testing
not provided	unknown	yes	not provided	not provided	not provided	not provided	not provided	research

Citations

PubMed

Massive sequencing of 70 genes reveals a myriad of missing genes or mechanisms to be uncovered in hereditary spastic paraplegias.

Morais S, Raymond L, Mairey M, Coutinho P, Brandão E, Ribeiro P, Loureiro JL, Sequeiros J, Brice A, Alonso I, Stevanin G.

Eur J Hum Genet. 2017 Nov;25(11):1217-1228. doi: 10.1038/ejhg.2017.124. Epub 2017 Aug 23.

PubMed [citation]

PMID:: 28832565
PMCID:: PMC5643959

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 Unit for Genetic & Epidemiological Research on Neurological Disorders, Instituto de Investigação e Inovação em Saúde, SCV000574507.1

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

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

From Genome Diagnostics Laboratory, The Hospital for Sick Children, SCV002106171.1

#	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	yes	not provided	not provided	not provided		not provided	not provided	not provided	not provided

Last Updated: Dec 24, 2023

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