NM_006612.6(KIF1C):c.2303G>A (p.Arg768Gln) AND Spastic ataxia 2

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Aug 5, 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:: RCV001915186.4

Allele description [Variation Report for NM_006612.6(KIF1C):c.2303G>A (p.Arg768Gln)]

NM_006612.6(KIF1C):c.2303G>A (p.Arg768Gln)

Gene:

KIF1C:kinesin family member 1C [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

17p13.2

Genomic location:

Preferred name:

NM_006612.6(KIF1C):c.2303G>A (p.Arg768Gln)

HGVS:

NC_000017.11:g.5022384G>A
NG_034137.1:g.29437G>A
NM_006612.6:c.2303G>AMANE SELECT
NP_006603.2:p.Arg768Gln
NC_000017.10:g.4925679G>A

Protein change:

R768Q

Links:

dbSNP: rs552440254

NCBI 1000 Genomes Browser:

rs552440254

Molecular consequence:

NM_006612.6:c.2303G>A - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Name:: Spastic ataxia 2
Synonyms:: Ataxia, spastic, 2, autosomal recessive
Identifiers:: MONDO: MONDO:0012651; MedGen: C1969796; Orphanet: 397946; OMIM: 611302

Recent activity

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polygalacturonase-like protein [Agrobacterium fabrum str. C58]
polygalacturonase-like protein [Agrobacterium fabrum str. C58]
gi|15160276|gb|AAK90257.1|

Protein
hypothetical protein AN8327.2 [Aspergillus nidulans FGSC A4]
hypothetical protein AN8327.2 [Aspergillus nidulans FGSC A4]
gi|40747794|gb|EAA66950.1||gnl|WGS: AN8327.2

Protein
ANIA_08761 [Aspergillus nidulans FGSC A4]
ANIA_08761 [Aspergillus nidulans FGSC A4]
Gene ID:2868323

Gene

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV002175290	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (Aug 5, 2021)	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

SCV002175290

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(Aug 5, 2021)

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, SCV002175290.3

#	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. Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant may create or strengthen a splice site. Algorithms developed to predict the effect of missense changes on protein structure and function are either unavailable or do not agree on the potential impact of this missense change (SIFT: "Deleterious"; PolyPhen-2: "Possibly Damaging"; Align-GVGD: "Class C0"). This variant has not been reported in the literature in individuals affected with KIF1C-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 ExAC database. This sequence change replaces arginine with glutamine at codon 768 of the KIF1C protein (p.Arg768Gln). The arginine residue is highly conserved and there is a small physicochemical difference between arginine and glutamine.

#	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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