NM_001195248.2(APTX):c.484-25_484-4del AND not provided

This record was updated by the submitter. Please see the current version.

Germline classification:: Benign (2 submissions)
Last evaluated:: Oct 27, 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:: RCV000676809.9

Allele description

NM_001195248.2(APTX):c.484-25_484-4del

Gene:

APTX:aprataxin [Gene - OMIM - HGNC]

Variant type:

Deletion

Cytogenetic location:

9p21.1

Genomic location:

Preferred name:

NM_001195248.2(APTX):c.484-25_484-4del

HGVS:

NC_000009.11:g.32986032_32986053del
NC_000009.12:g.32986043_32986064del
NG_012821.2:g.44077_44098del
NM_001195248.2:c.484-25_484-4delMANE SELECT
NM_001195249.2:c.484-25_484-4del
NM_001195250.2:c.322-25_322-4del
NM_001195251.2:c.484-25_484-4del
NM_001195252.2:c.268-25_268-4del
NM_001195254.2:c.322-25_322-4del
NM_001368995.1:c.484-25_484-4del
NM_001368996.1:c.484-25_484-4del
NM_001368997.1:c.484-25_484-4del
NM_001368998.1:c.484-25_484-4del
NM_001368999.1:c.484-25_484-4del
NM_001369000.1:c.322-25_322-4del
NM_001369001.1:c.322-25_322-4del
NM_001369002.1:c.220-25_220-4del
NM_001369003.1:c.220-25_220-4del
NM_001369004.1:c.220-25_220-4del
NM_001369005.1:c.220-25_220-4del
NM_001369006.1:c.220-25_220-4del
NM_001370669.1:c.220-25_220-4del
NM_001370670.1:c.220-25_220-4del
NM_001370673.1:c.220-25_220-4del
NM_175069.3:c.484-25_484-4del
NM_175073.3:c.484-25_484-4del
NC_000009.11:g.32986032_32986053del
NC_000009.11:g.32986041_32986062del
NC_000009.11:g.32986041_32986062del
NC_000009.11:g.32986041_32986062delCAAAAAAAAAAACAAAAAAAAA
NM_001195249.1:c.484-25_484-4delGTTTTTTTTTTTGTTTTTTTTT

Links:

dbSNP: rs778542759

NCBI 1000 Genomes Browser:

rs778542759

Molecular consequence:

NM_001195248.2:c.484-25_484-4del - intron variant - [Sequence Ontology: SO:0001627]
NM_001195249.2:c.484-25_484-4del - intron variant - [Sequence Ontology: SO:0001627]
NM_001195250.2:c.322-25_322-4del - intron variant - [Sequence Ontology: SO:0001627]
NM_001195251.2:c.484-25_484-4del - intron variant - [Sequence Ontology: SO:0001627]
NM_001195252.2:c.268-25_268-4del - intron variant - [Sequence Ontology: SO:0001627]
NM_001195254.2:c.322-25_322-4del - intron variant - [Sequence Ontology: SO:0001627]
NM_001368995.1:c.484-25_484-4del - intron variant - [Sequence Ontology: SO:0001627]
NM_001368996.1:c.484-25_484-4del - intron variant - [Sequence Ontology: SO:0001627]
NM_001368997.1:c.484-25_484-4del - intron variant - [Sequence Ontology: SO:0001627]
NM_001368998.1:c.484-25_484-4del - intron variant - [Sequence Ontology: SO:0001627]
NM_001368999.1:c.484-25_484-4del - intron variant - [Sequence Ontology: SO:0001627]
NM_001369000.1:c.322-25_322-4del - intron variant - [Sequence Ontology: SO:0001627]
NM_001369001.1:c.322-25_322-4del - intron variant - [Sequence Ontology: SO:0001627]
NM_001369002.1:c.220-25_220-4del - intron variant - [Sequence Ontology: SO:0001627]
NM_001369003.1:c.220-25_220-4del - intron variant - [Sequence Ontology: SO:0001627]
NM_001369004.1:c.220-25_220-4del - intron variant - [Sequence Ontology: SO:0001627]
NM_001369005.1:c.220-25_220-4del - intron variant - [Sequence Ontology: SO:0001627]
NM_001369006.1:c.220-25_220-4del - intron variant - [Sequence Ontology: SO:0001627]
NM_001370669.1:c.220-25_220-4del - intron variant - [Sequence Ontology: SO:0001627]
NM_001370670.1:c.220-25_220-4del - intron variant - [Sequence Ontology: SO:0001627]
NM_001370673.1:c.220-25_220-4del - intron variant - [Sequence Ontology: SO:0001627]
NM_175069.3:c.484-25_484-4del - intron variant - [Sequence Ontology: SO:0001627]
NM_175073.3:c.484-25_484-4del - intron variant - [Sequence Ontology: SO:0001627]

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
SCV000802618	Mayo Clinic Laboratories, Mayo Clinic	no assertion criteria provided	Benign (Feb 22, 2016)	unknown	clinical testing
SCV002353458	Invitae	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Benign (Oct 27, 2023)	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

SCV000802618

Mayo Clinic Laboratories, Mayo Clinic

no assertion criteria provided

Benign
(Feb 22, 2016)

unknown

clinical testing

SCV002353458

Invitae

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Benign
(Oct 27, 2023)

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	unknown	not provided	not provided	not provided	not provided	not provided	clinical testing
not provided	unknown	unknown	not provided	not provided	not provided	not provided	not provided	clinical testing

Citations

PubMed

Sherloc: a comprehensive refinement of the ACMG-AMP variant classification criteria.

Nykamp K, Anderson M, Powers M, Garcia J, Herrera B, Ho YY, Kobayashi Y, Patil N, Thusberg J, Westbrook M; Invitae Clinical Genomics Group., Topper S.

Genet Med. 2017 Oct;19(10):1105-1117. doi: 10.1038/gim.2017.37. Epub 2017 May 11. Erratum in: Genet Med. 2020 Jan;22(1):240. doi: 10.1038/s41436-019-0624-9.

PubMed [citation]

PMID:: 28492532
PMCID:: PMC5632818

Details of each submission

From Mayo Clinic Laboratories, Mayo Clinic, SCV000802618.1

#	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 Invitae, SCV002353458.3

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

Last Updated: Feb 28, 2024

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