NM_152594.3(SPRED1):c.807T>G (p.Asn269Lys) AND not provided

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Jul 30, 2018
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:: RCV000343889.2

Allele description [Variation Report for NM_152594.3(SPRED1):c.807T>G (p.Asn269Lys)]

NM_152594.3(SPRED1):c.807T>G (p.Asn269Lys)

Gene:

SPRED1:sprouty related EVH1 domain containing 1 [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

15q14

Genomic location:

Preferred name:

NM_152594.3(SPRED1):c.807T>G (p.Asn269Lys)

HGVS:

NC_000015.10:g.38351136T>G
NG_008980.1:g.103286T>G
NM_152594.3:c.807T>GMANE SELECT
NP_689807.1:p.Asn269Lys
NC_000015.9:g.38643337T>G
NM_152594.2:c.807T>G

Protein change:

N269K

Links:

dbSNP: rs886041428

NCBI 1000 Genomes Browser:

rs886041428

Molecular consequence:

NM_152594.3:c.807T>G - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Synonyms:: none provided
Identifiers:: MedGen: C3661900

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000330071	GeneDx	criteria provided, single submitter (GeneDx Variant Classification (06012015))	Uncertain significance (Jul 30, 2018)	germline	clinical testing	Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000330071

GeneDx

criteria provided, single submitter

(GeneDx Variant Classification (06012015))

Uncertain significance
(Jul 30, 2018)

germline

clinical testing

Citation Link

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

Details of each submission

From GeneDx, SCV000330071.7

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

Description

The N269K variant has not been published as a pathogenic variant, nor has it been reported as a benign variant to our knowledge. The variant is observed in 1/24022 (0.0042%) alleles from individuals of African background in large population cohorts (Lek et al., 2016). N269K is a semi-conservative amino acid substitution, which may impact secondary protein structure as these residues differ in some properties. In-silico analyses, including protein predictors and evolutionary conservation, support that this variant does not alter protein structure/function. In summary, based on the currently available information, it is unclear whether this variant is a pathogenic variant or a rare benign variant.

#	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 10, 2024

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