NM_001244008.2(KIF1A):c.3487T>A (p.Ser1163Thr) AND multiple conditions

Germline classification:: Likely benign (1 submission)
Last evaluated:: Jan 28, 2024
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:: RCV000525465.10

Allele description [Variation Report for NM_001244008.2(KIF1A):c.3487T>A (p.Ser1163Thr)]

NM_001244008.2(KIF1A):c.3487T>A (p.Ser1163Thr)

Gene:

KIF1A:kinesin family member 1A [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

2q37.3

Genomic location:

Preferred name:

NM_001244008.2(KIF1A):c.3487T>A (p.Ser1163Thr)

HGVS:

NC_000002.12:g.240744039A>T
NG_029724.1:g.81169T>A
NM_001244008.2:c.3487T>AMANE SELECT
NM_001320705.2:c.3211T>A
NM_001330289.2:c.3211T>A
NM_001330290.2:c.3286T>A
NM_001379631.1:c.3562T>A
NM_001379632.1:c.3436T>A
NM_001379633.1:c.3460T>A
NM_001379634.1:c.3286T>A
NM_001379635.1:c.3286T>A
NM_001379636.1:c.3184T>A
NM_001379637.1:c.3259T>A
NM_001379638.1:c.3211T>A
NM_001379639.1:c.3184T>A
NM_001379640.1:c.3181T>A
NM_001379641.1:c.3184T>A
NM_001379642.1:c.3460T>A
NM_001379645.1:c.3460T>A
NM_001379646.1:c.3286T>A
NM_001379648.1:c.3259T>A
NM_001379649.1:c.3184T>A
NM_001379650.1:c.3184T>A
NM_001379651.1:c.3184T>A
NM_001379653.1:c.3184T>A
NM_004321.7:c.3184T>A
NM_004321.8:c.3184T>A
NP_001230937.1:p.Ser1163Thr
NP_001307634.1:p.Ser1071Thr
NP_001317218.1:p.Ser1071Thr
NP_001317219.1:p.Ser1096Thr
NP_001366560.1:p.Ser1188Thr
NP_001366561.1:p.Ser1146Thr
NP_001366562.1:p.Ser1154Thr
NP_001366563.1:p.Ser1096Thr
NP_001366564.1:p.Ser1096Thr
NP_001366565.1:p.Ser1062Thr
NP_001366566.1:p.Ser1087Thr
NP_001366567.1:p.Ser1071Thr
NP_001366568.1:p.Ser1062Thr
NP_001366569.1:p.Ser1061Thr
NP_001366570.1:p.Ser1062Thr
NP_001366571.1:p.Ser1154Thr
NP_001366574.1:p.Ser1154Thr
NP_001366575.1:p.Ser1096Thr
NP_001366577.1:p.Ser1087Thr
NP_001366578.1:p.Ser1062Thr
NP_001366579.1:p.Ser1062Thr
NP_001366580.1:p.Ser1062Thr
NP_001366582.1:p.Ser1062Thr
NP_004312.2:p.Ser1062Thr
LRG_367t2:c.3184T>A
LRG_367:g.81169T>A
NC_000002.11:g.241683456A>T
NM_004321.5:c.3184T>A
NM_004321.6:c.3184T>A

Protein change:

S1061T

Links:

dbSNP: rs527346259

NCBI 1000 Genomes Browser:

rs527346259

Molecular consequence:

NM_001244008.2:c.3487T>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001320705.2:c.3211T>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001330289.2:c.3211T>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001330290.2:c.3286T>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001379631.1:c.3562T>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001379632.1:c.3436T>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001379633.1:c.3460T>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001379634.1:c.3286T>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001379635.1:c.3286T>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001379636.1:c.3184T>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001379637.1:c.3259T>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001379638.1:c.3211T>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001379639.1:c.3184T>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001379640.1:c.3181T>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001379641.1:c.3184T>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001379642.1:c.3460T>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001379645.1:c.3460T>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001379646.1:c.3286T>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001379648.1:c.3259T>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001379649.1:c.3184T>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001379650.1:c.3184T>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001379651.1:c.3184T>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001379653.1:c.3184T>A - missense variant - [Sequence Ontology: SO:0001583]
NM_004321.8:c.3184T>A - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Name:: Hereditary spastic paraplegia 30
Synonyms:: Spastic paraplegia 30, autosomal recessive; SPASTIC PARAPLEGIA 30A, AUTOSOMAL DOMINANT
Identifiers:: MONDO: MONDO:0012476; MedGen: C5235139; Orphanet: 101010; OMIM: 610357

Name:: Neuropathy, hereditary sensory, type 2C
Synonyms:: Hereditary sensory and autonomic neuropathy type IIC
Identifiers:: MONDO: MONDO:0013634; MedGen: C3280168; Orphanet: 970; OMIM: 614213

Name:: Intellectual disability, autosomal dominant 9 (NESCAVS)
Synonyms:: Mental retardation, autosomal dominant 9; NESCAV SYNDROME
Identifiers:: MONDO: MONDO:0013656; MedGen: C5393830; OMIM: 614255

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000638576	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Likely benign (Jan 28, 2024)	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

SCV000638576

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Likely benign
(Jan 28, 2024)

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, SCV000638576.7

#	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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