NM_014946.4(SPAST):c.1209del (p.Phe404fs) AND not provided

Germline classification:: Likely pathogenic (2 submissions)
Last evaluated:: Sep 30, 2016
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:: RCV000423551.3

Allele description [Variation Report for NM_014946.4(SPAST):c.1209del (p.Phe404fs)]

NM_014946.4(SPAST):c.1209del (p.Phe404fs)

Gene:

SPAST:spastin [Gene - OMIM - HGNC]

Variant type:

Deletion

Cytogenetic location:

2p22.3

Genomic location:

Preferred name:

NM_014946.4(SPAST):c.1209del (p.Phe404fs)

HGVS:

NC_000002.12:g.32128443del
NG_008730.1:g.69833del
NM_001363823.2:c.1206del
NM_001363875.2:c.1110del
NM_001377959.1:c.1113del
NM_014946.4:c.1209delMANE SELECT
NM_199436.2:c.1113del
NP_001350752.1:p.Phe403fs
NP_001350804.1:p.Phe371fs
NP_001364888.1:p.Phe372fs
NP_055761.2:p.Phe404fs
NP_055761.2:p.Phe404fs
NP_955468.1:p.Phe372fs
LRG_714t1:c.1209del
LRG_714:g.69833del
LRG_714p1:p.Phe404fs
NC_000002.11:g.32353512del
NM_014946.3:c.1209del
p.Phe404Leufs*3

Protein change:

F371fs

Links:

dbSNP: rs1057520127

NCBI 1000 Genomes Browser:

rs1057520127

Molecular consequence:

NM_001363823.2:c.1206del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001363875.2:c.1110del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001377959.1:c.1113del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_014946.4:c.1209del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_199436.2:c.1113del - frameshift variant - [Sequence Ontology: SO:0001589]

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
SCV000511225	Center for Pediatric Genomic Medicine, Children's Mercy Hospital and Clinics	criteria provided, single submitter (ACMG Guidelines, 2015)	Likely pathogenic (Sep 1, 2016)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]
SCV000615384	Athena Diagnostics	criteria provided, single submitter (Athena Diagnostics Criteria)	Likely pathogenic (Sep 30, 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

SCV000511225

Center for Pediatric Genomic Medicine, Children's Mercy Hospital and Clinics

criteria provided, single submitter

(ACMG Guidelines, 2015)

Likely pathogenic
(Sep 1, 2016)

germline

clinical testing

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

SCV000615384

Athena Diagnostics

criteria provided, single submitter

(Athena Diagnostics Criteria)

Likely pathogenic
(Sep 30, 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	not provided	not provided	not provided	not provided	not provided	not provided	clinical testing
not provided	germline	unknown	not provided	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

A Standardized DNA Variant Scoring System for Pathogenicity Assessments in Mendelian Disorders.

Karbassi I, Maston GA, Love A, DiVincenzo C, Braastad CD, Elzinga CD, Bright AR, Previte D, Zhang K, Rowland CM, McCarthy M, Lapierre JL, Dubois F, Medeiros KA, Batish SD, Jones J, Liaquat K, Hoffman CA, Jaremko M, Wang Z, Sun W, Buller-Burckle A, et al.

Hum Mutat. 2016 Jan;37(1):127-34. doi: 10.1002/humu.22918. Epub 2015 Oct 29.

PubMed [citation]

PMID:: 26467025
PMCID:: PMC4737317

Details of each submission

From Center for Pediatric Genomic Medicine, Children's Mercy Hospital and Clinics, SCV000511225.1

#	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	not provided	not provided	not provided	not provided		not provided	0.000232	not provided	not provided

From Athena Diagnostics, SCV000615384.1

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

Last Updated: Sep 29, 2024

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