NM_022089.4(ATP13A2):c.3057del (p.Tyr1020fs) AND Autosomal recessive spastic paraplegia type 78

Germline classification:: Pathogenic (2 submissions)
Last evaluated:: Jun 30, 2022
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:: RCV002509424.2

Allele description [Variation Report for NM_022089.4(ATP13A2):c.3057del (p.Tyr1020fs)]

NM_022089.4(ATP13A2):c.3057del (p.Tyr1020fs)

Gene:

ATP13A2:ATPase cation transporting 13A2 [Gene - OMIM - HGNC]

Variant type:

Deletion

Cytogenetic location:

1p36.13

Genomic location:

Preferred name:

NM_022089.4(ATP13A2):c.3057del (p.Tyr1020fs)

Other names:

p.Tyr1020Thrfs*3

HGVS:

NC_000001.11:g.16987072del
NG_009054.1:g.29857del
NM_001141973.3:c.3042del
NM_001141974.3:c.2925del
NM_022089.4:c.3057delMANE SELECT
NP_001135445.1:p.Tyr1015fs
NP_001135446.1:p.Tyr976fs
NP_071372.1:p.Tyr1020fs
LRG_834t1:c.3057del
LRG_834:g.29857del
LRG_834p1:p.Tyr1020fs
NC_000001.10:g.17313567del
NM_022089.2:c.3057del
NM_022089.2:c.3057delC
NM_022089.3:c.3057del
NM_022089.3:c.3057delC
p.Y1020Tfs*3

Protein change:

Y1015fs

Links:

OMIM: 610513.0001; dbSNP: rs765632065

NCBI 1000 Genomes Browser:

rs765632065

Molecular consequence:

NM_001141973.3:c.3042del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001141974.3:c.2925del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_022089.4:c.3057del - frameshift variant - [Sequence Ontology: SO:0001589]

Observations:

Condition(s)

Name:: Autosomal recessive spastic paraplegia type 78
Identifiers:: MONDO: MONDO:0014975; MedGen: C5567893; OMIM: 617225

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV002818543	Undiagnosed Diseases Network, NIH - Undiagnosed Diseases Network (NIH), UDN	no assertion criteria provided	Pathogenic (Jul 12, 2022)	paternal	clinical testing
SCV003835240	Baylor Genetics	criteria provided, single submitter (ACMG Guidelines, 2015)	Pathogenic (Jun 30, 2022)	unknown	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

SCV002818543

Undiagnosed Diseases Network, NIH - Undiagnosed Diseases Network (NIH), UDN

no assertion criteria provided

Pathogenic
(Jul 12, 2022)

paternal

clinical testing

SCV003835240

Baylor Genetics

criteria provided, single submitter

(ACMG Guidelines, 2015)

Pathogenic
(Jun 30, 2022)

unknown

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	unknown	unknown	not provided	not provided	not provided	not provided	not provided	clinical testing
not provided	paternal	yes	1	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 Undiagnosed Diseases Network, NIH - Undiagnosed Diseases Network (NIH), UDN, SCV002818543.1

#	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	paternal	yes	not provided	Blood	not provided		1	not provided	not provided	not provided

From Baylor Genetics, SCV003835240.1

#	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	unknown	unknown	not provided	not provided	not provided		not provided	not provided	not provided	not provided

Last Updated: Nov 30, 2024

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