NM_144599.5(NIPA1):c.21_35del (p.Ala12_Ala16del) AND Hereditary spastic paraplegia 6

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

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Jul 17, 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:: RCV003603968.1

Allele description

NM_144599.5(NIPA1):c.21_35del (p.Ala12_Ala16del)

Genes:

LOC130056709:ATAC-STARR-seq lymphoblastoid silent region 6259 [Gene]
NIPA1:NIPA magnesium transporter 1 [Gene - OMIM - HGNC]

Variant type:

Deletion

Cytogenetic location:

15q11.2

Genomic location:

Preferred name:

NM_144599.5(NIPA1):c.21_35del (p.Ala12_Ala16del)

HGVS:

NC_000015.10:g.22786677_22786691del
NG_009056.1:g.5453_5467del
NG_191130.1:g.266_280del
NM_001142275.1:c.-48+429_-48+443del
NM_144599.5:c.21_35delMANE SELECT
NP_653200.2:p.Ala12_Ala16del
NC_000015.9:g.23086377_23086391del
NC_000015.9:g.23086382_23086396del

Molecular consequence:

NM_144599.5:c.21_35del - inframe_deletion - [Sequence Ontology: SO:0001822]
NM_001142275.1:c.-48+429_-48+443del - intron variant - [Sequence Ontology: SO:0001627]

Condition(s)

Name:: Hereditary spastic paraplegia 6 (SPG6)
Synonyms:: SPASTIC PARAPLEGIA 6, AUTOSOMAL DOMINANT; Spastic paraplegia 6; Familial spastic paraplegia autosomal dominant 3
Identifiers:: MONDO: MONDO:0010878; MedGen: C1838192; Orphanet: 100988; OMIM: 600363

Recent activity

Clear Turn Off Turn On

Human ras-related small GTP binding protein Rab5 (rab5) mRNA, complete cds
Human ras-related small GTP binding protein Rab5 (rab5) mRNA, complete cds
gi|642531|gb|U18420.1|HSU18420

Nucleotide
Homo sapiens signal transducer and activator of transcription (STAT5) mRNA, comp...
Homo sapiens signal transducer and activator of transcription (STAT5) mRNA, complete cds
gi|736682|gb|L41142.1|HUMSTAT5A

Nucleotide
Human Rab5c-like protein mRNA, complete cds
Human Rab5c-like protein mRNA, complete cds
gi|508284|gb|U11293.1|HSU11293

Nucleotide
Human signal transducer and activator of transcription Stat5B mRNA, complete cds
Human signal transducer and activator of transcription Stat5B mRNA, complete cds
gi|1330323|gb|U47686.1|HSU47686

Nucleotide

Your browsing activity is empty.

Activity recording is turned off.

Turn recording back on

Help

Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV004549576	Invitae	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (Jul 17, 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

SCV004549576

Invitae

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(Jul 17, 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

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 Invitae, SCV004549576.1

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

Description

In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. Experimental studies and prediction algorithms are not available or were not evaluated, and the functional significance of this variant is currently unknown. This variant has not been reported in the literature in individuals affected with NIPA1-related conditions. The frequency data for this variant in the population databases is considered unreliable, as metrics indicate poor data quality at this position in the gnomAD database. This variant, c.21_35del, results in the deletion of 5 amino acid(s) of the NIPA1 protein (p.Ala12_Ala16del), but otherwise preserves the integrity of the reading frame.

#	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

ClinVar

Relating variation to medicine