NM_152594.3(SPRED1):c.892G>C (p.Asp298His) AND Legius syndrome

Clinical significance:Uncertain significance (Last evaluated: Dec 20, 2019)

Review status:1 star out of maximum of 4 stars

criteria provided, single submitter

Based on:
1 submission [Details]
Record status:

Allele description [Variation Report for NM_152594.3(SPRED1):c.892G>C (p.Asp298His)]

NM_152594.3(SPRED1):c.892G>C (p.Asp298His)

SPRED1:sprouty related EVH1 domain containing 1 [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
Genomic location:
Preferred name:
NM_152594.3(SPRED1):c.892G>C (p.Asp298His)
  • NC_000015.10:g.38351221G>C
  • NG_008980.1:g.103371G>C
  • NM_152594.3:c.892G>CMANE SELECT
  • NP_689807.1:p.Asp298His
  • NC_000015.9:g.38643422G>C
  • NM_152594.2:c.892G>C
Protein change:
Molecular consequence:
  • NM_152594.3:c.892G>C - missense variant - [Sequence Ontology: SO:0001583]


Legius syndrome (LGSS)
Neurofibromatosis type 1 like syndrome
MONDO: MONDO:0012669; MedGen: C1969623; Orphanet: 137605; OMIM: 611431

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
SCV001227245Invitaecriteria provided, single submitter
Uncertain significance
(Dec 20, 2019)
germlineclinical testing

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

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineunknownnot providednot providednot providednot providednot providedclinical testing



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):240-242.

PubMed [citation]

Details of each submission

From Invitae, SCV001227245.2

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (1)


This sequence change replaces aspartic acid with histidine at codon 298 of the SPRED1 protein (p.Asp298His). The aspartic acid residue is moderately conserved and there is a moderate physicochemical difference between aspartic acid and histidine. The frequency data for this variant in the population databases is considered unreliable, as metrics indicate poor data quality at this position in the ExAC database. This variant has not been reported in the literature in individuals with SPRED1-related disease. Algorithms developed to predict the effect of missense changes on protein structure and function do not agree on the potential impact of this missense change (SIFT: Deleterious; PolyPhen-2: Possibly Damaging; Align-GVGD: Class C0). In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance.

OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknownnot providednot providednot providednot providednot providednot providednot provided

Last Updated: Oct 7, 2021

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