NM_001244008.2(KIF1A):c.232G>A (p.Gly78Ser) AND Hereditary spastic paraplegia 30

Germline classification:: Pathogenic/Likely pathogenic (3 submissions)
Last evaluated:: Nov 19, 2024
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:: RCV001251219.3

Allele description [Variation Report for NM_001244008.2(KIF1A):c.232G>A (p.Gly78Ser)]

NM_001244008.2(KIF1A):c.232G>A (p.Gly78Ser)

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.232G>A (p.Gly78Ser)

HGVS:

NC_000002.12:g.240788182C>T
NG_029724.1:g.37026G>A
NM_001244008.2:c.232G>AMANE SELECT
NM_001320705.2:c.232G>A
NM_001330289.2:c.232G>A
NM_001330290.2:c.232G>A
NM_001379631.1:c.232G>A
NM_001379632.1:c.232G>A
NM_001379633.1:c.232G>A
NM_001379634.1:c.232G>A
NM_001379635.1:c.232G>A
NM_001379636.1:c.232G>A
NM_001379637.1:c.232G>A
NM_001379638.1:c.232G>A
NM_001379639.1:c.232G>A
NM_001379640.1:c.232G>A
NM_001379641.1:c.232G>A
NM_001379642.1:c.232G>A
NM_001379645.1:c.232G>A
NM_001379646.1:c.232G>A
NM_001379648.1:c.232G>A
NM_001379649.1:c.232G>A
NM_001379650.1:c.232G>A
NM_001379651.1:c.232G>A
NM_001379653.1:c.232G>A
NM_004321.8:c.232G>A
NP_001230937.1:p.Gly78Ser
NP_001230937.1:p.Gly78Ser
NP_001307634.1:p.Gly78Ser
NP_001317218.1:p.Gly78Ser
NP_001317219.1:p.Gly78Ser
NP_001366560.1:p.Gly78Ser
NP_001366561.1:p.Gly78Ser
NP_001366562.1:p.Gly78Ser
NP_001366563.1:p.Gly78Ser
NP_001366564.1:p.Gly78Ser
NP_001366565.1:p.Gly78Ser
NP_001366566.1:p.Gly78Ser
NP_001366567.1:p.Gly78Ser
NP_001366568.1:p.Gly78Ser
NP_001366569.1:p.Gly78Ser
NP_001366570.1:p.Gly78Ser
NP_001366571.1:p.Gly78Ser
NP_001366574.1:p.Gly78Ser
NP_001366575.1:p.Gly78Ser
NP_001366577.1:p.Gly78Ser
NP_001366578.1:p.Gly78Ser
NP_001366579.1:p.Gly78Ser
NP_001366580.1:p.Gly78Ser
NP_001366582.1:p.Gly78Ser
NP_004312.2:p.Gly78Ser
NP_004312.2:p.Gly78Ser
LRG_367t1:c.232G>A
LRG_367t2:c.232G>A
LRG_367:g.37026G>A
LRG_367p1:p.Gly78Ser
LRG_367p2:p.Gly78Ser
NC_000002.11:g.241727599C>T
NM_001244008.1:c.232G>A
NM_004321.7:c.232G>A

Protein change:

G78S

Links:

dbSNP: rs1057518760

NCBI 1000 Genomes Browser:

rs1057518760

Molecular consequence:

NM_001244008.2:c.232G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001320705.2:c.232G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001330289.2:c.232G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001330290.2:c.232G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001379631.1:c.232G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001379632.1:c.232G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001379633.1:c.232G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001379634.1:c.232G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001379635.1:c.232G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001379636.1:c.232G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001379637.1:c.232G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001379638.1:c.232G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001379639.1:c.232G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001379640.1:c.232G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001379641.1:c.232G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001379642.1:c.232G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001379645.1:c.232G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001379646.1:c.232G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001379648.1:c.232G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001379649.1:c.232G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001379650.1:c.232G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001379651.1:c.232G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001379653.1:c.232G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_004321.8:c.232G>A - missense variant - [Sequence Ontology: SO:0001583]

Observations:

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

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV001426708	SIB Swiss Institute of Bioinformatics	criteria provided, single submitter (ACMG Guidelines, 2015)	Likely pathogenic (Jun 15, 2020)	unknown	curation	PubMed (2) [See all records that cite these PMIDs] 31488895, 25741868
SCV001451078	Paris Brain Institute, Inserm - ICM	criteria provided, single submitter (ACMG Guidelines, 2015)	Pathogenic	unknown	clinical testing	PubMed (1) [See all records that cite this PMID]
SCV005400661	Institute of Medical Genetics and Applied Genomics, University Hospital Tübingen	criteria provided, single submitter (ACMG Guidelines, 2015)	Likely pathogenic (Nov 19, 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

SCV001426708

SIB Swiss Institute of Bioinformatics

criteria provided, single submitter

(ACMG Guidelines, 2015)

Likely pathogenic
(Jun 15, 2020)

unknown

curation

PubMed (2)
[See all records that cite these PMIDs]

SCV001451078

Paris Brain Institute, Inserm - ICM

criteria provided, single submitter

(ACMG Guidelines, 2015)

Pathogenic

unknown

clinical testing

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

SCV005400661

Institute of Medical Genetics and Applied Genomics, University Hospital Tübingen

criteria provided, single submitter

(ACMG Guidelines, 2015)

Likely pathogenic
(Nov 19, 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	unknown	unknown	not provided	not provided	not provided	not provided	not provided	curation
not provided	unknown	yes	2	not provided	not provided	not provided	not provided	clinical testing
not provided	germline	yes	not provided	not provided	not provided	not provided	not provided	clinical testing

Citations

PubMed

KIF1A variants are a frequent cause of autosomal dominant hereditary spastic paraplegia.

Pennings M, Schouten MI, van Gaalen J, Meijer RPP, de Bot ST, Kriek M, Saris CGJ, van den Berg LH, van Es MA, Zuidgeest DMH, Elting MW, van de Kamp JM, van Spaendonck-Zwarts KY, Die-Smulders C, Brilstra EH, Verschuuren CC, de Vries BBA, Bruijn J, Sofou K, Duijkers FA, Jaeger B, Schieving JH, et al.

Eur J Hum Genet. 2020 Jan;28(1):40-49. doi: 10.1038/s41431-019-0497-z. Epub 2019 Sep 5.

PubMed [citation]

PMID:: 31488895
PMCID:: PMC6906463

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

Details of each submission

From SIB Swiss Institute of Bioinformatics, SCV001426708.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	curation	PubMed (2)

Description

This variant is interpreted as likely pathogenic for spastic paraplegia 30, autosomal dominant. The following ACMG Tag(s) were applied: Absent from controls (or at extremely low frequency if recessive) in Exome Sequencing Project, 1000 Genomes Project, or Exome Aggregation Consortium (PM2); De novo (paternity and maternity confirmed) (PS2 downgraded to moderate); Multiple lines of computational evidence support a deleterious effect on the gene or gene product (PP3); Missense variant in a gene that has a low rate of benign missense variation and in which missense variants are a common mechanism of disease (PP2).

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	unknown	unknown	not provided	not provided	not provided		not provided	not provided	not provided	not provided

From Paris Brain Institute, Inserm - ICM, SCV001451078.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	2	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	unknown	yes	not provided	not provided	not provided		2	not provided	not provided	not provided

From Institute of Medical Genetics and Applied Genomics, University Hospital Tübingen, SCV005400661.1

#	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	yes	not provided	not provided	not provided		not provided	not provided	not provided	not provided

Last Updated: Nov 30, 2024

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