NM_004984.4(KIF5A):c.2945C>T (p.Ser982Phe) AND Spastic paraplegia

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Mar 29, 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:: RCV002037097.4

Allele description [Variation Report for NM_004984.4(KIF5A):c.2945C>T (p.Ser982Phe)]

NM_004984.4(KIF5A):c.2945C>T (p.Ser982Phe)

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.2945C>T (p.Ser982Phe)

HGVS:

NC_000012.12:g.57581905C>T
NG_008155.1:g.36842C>T
NM_001354705.2:c.2678C>T
NM_004984.4:c.2945C>TMANE SELECT
NP_001341634.1:p.Ser893Phe
NP_004975.2:p.Ser982Phe
NC_000012.11:g.57975688C>T

Protein change:

S893F

Links:

dbSNP: rs1211468940

NCBI 1000 Genomes Browser:

rs1211468940

Molecular consequence:

NM_001354705.2:c.2678C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_004984.4:c.2945C>T - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

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

Recent activity

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RecName: Full=BAG family molecular chaperone regulator 2; Short=BAG-2; AltName: ...
RecName: Full=BAG family molecular chaperone regulator 2; Short=BAG-2; AltName: Full=Bcl-2-associated athanogene 2
gi|12229698|sp|O95816.1|BAG2_HUMAN

Protein
RecName: Full=Leukotriene C4 synthase; Short=LTC4 synthase; AltName: Full=Glutat...
RecName: Full=Leukotriene C4 synthase; Short=LTC4 synthase; AltName: Full=Glutathione S-transferase LTC4; AltName: Full=Leukotriene-C(4) synthase; AltName: Full=Leukotriene-C4 synthase
gi|2833283|sp|Q16873.1|LTC4S_HUMAN

Protein
Or4k15c olfactory receptor family 4 subfamily K member 15C [Mus musculus]
Or4k15c olfactory receptor family 4 subfamily K member 15C [Mus musculus]
Gene ID:258313

Gene

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV002111026	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (Mar 29, 2022)	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

SCV002111026

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(Mar 29, 2022)

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 Labcorp Genetics (formerly Invitae), Labcorp, SCV002111026.3

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

Description

This sequence change replaces serine, which is neutral and polar, with phenylalanine, which is neutral and non-polar, at codon 982 of the KIF5A protein (p.Ser982Phe). 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. Advanced modeling of protein sequence and biophysical properties (such as structural, functional, and spatial information, amino acid conservation, physicochemical variation, residue mobility, and thermodynamic stability) performed at Invitae indicates that this missense variant is not expected to disrupt KIF5A protein function. This variant has not been reported in the literature in individuals affected with KIF5A-related conditions. This variant is not present in population databases (gnomAD no frequency).

#	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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