NM_152594.3(SPRED1):c.30C>A (p.Asn10Lys) AND Legius syndrome

Germline classification:: Likely benign (2 submissions)
Last evaluated:: Jan 29, 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:: RCV000466135.16

Allele description [Variation Report for NM_152594.3(SPRED1):c.30C>A (p.Asn10Lys)]

NM_152594.3(SPRED1):c.30C>A (p.Asn10Lys)

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.30C>A (p.Asn10Lys)

HGVS:

NC_000015.10:g.38253215C>A
NG_008980.1:g.5365C>A
NM_152594.3:c.30C>AMANE SELECT
NP_689807.1:p.Asn10Lys
NC_000015.9:g.38545416C>A
NM_152594.2:c.30C>A

Protein change:

N10K

Links:

dbSNP: rs201692618

NCBI 1000 Genomes Browser:

rs201692618

Molecular consequence:

NM_152594.3:c.30C>A - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Name:: Legius syndrome
Synonyms:: Neurofibromatosis type 1 like syndrome
Identifiers:: MONDO: MONDO:0012669; MedGen: C1969623; Orphanet: 137605; OMIM: 611431

Recent activity

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ribosomal protein L23 (chloroplast) [Viburnum plicatum]
ribosomal protein L23 (chloroplast) [Viburnum plicatum]
gi|2651577024|gb|WRY70307.1|

Protein
Drimys confertifolia DNA, complete sequence, microsatellite: BCM1M
Drimys confertifolia DNA, complete sequence, microsatellite: BCM1M
gi|355330044|dbj|AB639954.1|

Nucleotide
nad3 [Acacia ligulata]
nad3 [Acacia ligulata]
Gene ID:39120471

Gene
rps10 [Acacia ligulata]
rps10 [Acacia ligulata]
Gene ID:39120460

Gene

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000560563	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Likely benign (Jan 29, 2024)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]
SCV001278000	Illumina Laboratory Services, Illumina	criteria provided, single submitter (ICSL Variant Classification Criteria 13 December 2019)	Likely benign (Apr 27, 2017)	germline	clinical testing	PubMed (1) [See all records that cite this PMID] Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000560563

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Likely benign
(Jan 29, 2024)

germline

clinical testing

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

SCV001278000

Illumina Laboratory Services, Illumina

criteria provided, single submitter

(ICSL Variant Classification Criteria 13 December 2019)

Likely benign
(Apr 27, 2017)

germline

clinical testing

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

Citation Link

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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

Review and update of SPRED1 mutations causing Legius syndrome.

Brems H, Pasmant E, Van Minkelen R, Wimmer K, Upadhyaya M, Legius E, Messiaen L.

Hum Mutat. 2012 Nov;33(11):1538-46. doi: 10.1002/humu.22152. Epub 2012 Aug 1. Review.

PubMed [citation]

PMID:: 22753041

Details of each submission

From Labcorp Genetics (formerly Invitae), Labcorp, SCV000560563.8

#	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

From Illumina Laboratory Services, Illumina, SCV001278000.1

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

Description

This variant was observed as part of a predisposition screen in an ostensibly healthy population. A literature search was performed for the gene, cDNA change, and amino acid change (where applicable). Publications were found based on this search. The evidence from the literature, in combination with allele frequency data from public databases where available, was sufficient to determine this variant is unlikely to cause disease. Therefore, this variant is classified as likely benign.

#	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: Oct 8, 2024

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