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NM_004984.4(KIF5A):c.3020+1G>C AND Spastic paraplegia

Germline classification:
Pathogenic (1 submission)
Last evaluated:
Sep 9, 2021
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:
RCV001956486.4

Allele description [Variation Report for NM_004984.4(KIF5A):c.3020+1G>C]

NM_004984.4(KIF5A):c.3020+1G>C

Gene:
KIF5A:kinesin family member 5A [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
12q13.3
Genomic location:
Preferred name:
NM_004984.4(KIF5A):c.3020+1G>C
HGVS:
  • NC_000012.12:g.57582630G>C
  • NG_008155.1:g.37567G>C
  • NM_001354705.2:c.2753+1G>C
  • NM_004984.4:c.3020+1G>CMANE SELECT
  • NC_000012.11:g.57976413G>C
Links:
dbSNP: rs1555179091
NCBI 1000 Genomes Browser:
rs1555179091
Molecular consequence:
  • NM_001354705.2:c.2753+1G>C - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_004984.4:c.3020+1G>C - splice donor variant - [Sequence Ontology: SO:0001575]

Condition(s)

Name:
Spastic paraplegia
Identifiers:
MedGen: C0037772; Human Phenotype Ontology: HP:0001258

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV002242028Labcorp Genetics (formerly Invitae), Labcorp
criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))		Pathogenic
(Sep 9, 2021) 		germlineclinical testing

PubMed (5)
[See all records that cite these PMIDs]

Help

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineunknownnot providednot providednot providednot providednot providedclinical testing

Citations

PubMed

Aberrant 5' splice sites in human disease genes: mutation pattern, nucleotide structure and comparison of computational tools that predict their utilization.

Buratti E, Chivers M, Královicová J, Romano M, Baralle M, Krainer AR, Vorechovsky I.

Nucleic Acids Res. 2007;35(13):4250-63. Epub 2007 Jun 18.

PubMed [citation]
PMID:
17576681
PMCID:
PMC1934990

Statistical features of human exons and their flanking regions.

Zhang MQ.

Hum Mol Genet. 1998 May;7(5):919-32.

PubMed [citation]
PMID:
9536098
See all PubMed Citations (5)

Details of each submission

From Labcorp Genetics (formerly Invitae), Labcorp, SCV002242028.3

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (5)

Description

Variants that disrupt the consensus splice site are a relatively common cause of aberrant splicing (PMID: 17576681, 9536098). Studies have shown that this variant results in exon 27 skipping and introduces a new termination codon (PMID: 29566793). However the mRNA is not expected to undergo nonsense-mediated decay. For these reasons, this variant has been classified as Pathogenic. This variant has been observed in individuals with amyotrophic lateral sclerosis (PMID: 29342275, 29566793; Invitae). It has also been observed to segregate with disease in related individuals. This variant is not present in population databases (ExAC no frequency). This sequence change falls in intron 27 of the KIF5A gene. It does not directly change the encoded amino acid sequence of the KIF5A protein. RNA analysis indicates that this variant induces altered splicing and likely disrupts the C-terminus of the protein.

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknownnot providednot providednot providednot providednot providednot providednot provided

Last Updated: Sep 29, 2024