NM_198525.3(KIF7):c.733G>A (p.Val245Ile) AND Short-limb skeletal dysplasia with severe combined immunodeficiency

Germline classification:: Uncertain significance (1 submission)
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:: RCV001823576.3

Allele description [Variation Report for NM_198525.3(KIF7):c.733G>A (p.Val245Ile)]

NM_198525.3(KIF7):c.733G>A (p.Val245Ile)

Gene:

KIF7:kinesin family member 7 [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

15q26.1

Genomic location:

Preferred name:

NM_198525.3(KIF7):c.733G>A (p.Val245Ile)

HGVS:

NC_000015.10:g.89649164C>T
NG_030338.1:g.11288G>A
NM_198525.3:c.733G>AMANE SELECT
NP_940927.2:p.Val245Ile
NC_000015.9:g.90192395C>T
NM_198525.2:c.[733G>A]

Protein change:

V245I

Links:

dbSNP: rs1212811357

NCBI 1000 Genomes Browser:

rs1212811357

Molecular consequence:

NM_198525.3:c.733G>A - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Name:: Short-limb skeletal dysplasia with severe combined immunodeficiency
Synonyms:: Achondroplasia and severe combined immunodeficiency; Achondroplasia so-called and severe combined immunodeficiency
Identifiers:: MONDO: MONDO:0008704; MedGen: C1860168; OMIM: 200900

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV002073123	Neuberg Centre For Genomic Medicine, NCGM	criteria provided, single submitter (ACMG Guidelines, 2015)	Uncertain significance	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

SCV002073123

Neuberg Centre For Genomic Medicine, NCGM

criteria provided, single submitter

(ACMG Guidelines, 2015)

Uncertain significance

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	yes	not provided	not provided	not provided	not provided	not provided	clinical testing

Citations

PubMed

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 Neuberg Centre For Genomic Medicine, NCGM, SCV002073123.1

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

Description

The missense variant p.V245I in KIF7 (NM_198525.3) has not been reported previously as a pathogenic variant nor as a benign variant, to our knowledge. The p.V245I variant is observed in 1/54,200 (0.0018%) alleles from individuals of European (Non-Finnish) background in gnomAD Exomes and is novel (not in any individuals) in 1000 Genomes. The p.V245I missense variant is predicted to be tolerated by both SIFT or PolyPhen2. The nucleotide c.733 in KIF7 is not conserved according to a GERP++ and PhyloP analysis of 100 vertebrates. For these reasons, this variant has been classified as Uncertain Significance.

#	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: Apr 6, 2024

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