NM_006642.5(SDCCAG8):c.916G>A (p.Glu306Lys) AND multiple conditions

Clinical significance:Uncertain significance (Last evaluated: Mar 3, 2017)

Review status:1 star out of maximum of 4 stars

criteria provided, single submitter

Based on:
1 submission [Details]
Record status:
current
Accession:
RCV000531568.1

Allele description [Variation Report for NM_006642.5(SDCCAG8):c.916G>A (p.Glu306Lys)]

NM_006642.5(SDCCAG8):c.916G>A (p.Glu306Lys)

Gene:
SDCCAG8:SHH signaling and ciliogenesis regulator SDCCAG8 [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
1q43
Genomic location:
Preferred name:
NM_006642.5(SDCCAG8):c.916G>A (p.Glu306Lys)
HGVS:
  • NC_000001.11:g.243308164G>A
  • NG_027811.1:g.57160G>A
  • NM_001350246.1:c.13G>A
  • NM_001350247.1:c.13G>A
  • NM_001350248.1:c.1012G>A
  • NM_001350249.1:c.622G>A
  • NM_001350251.1:c.13G>A
  • NM_006642.5:c.916G>AMANE SELECT
  • NP_001337175.1:p.Glu5Lys
  • NP_001337176.1:p.Glu5Lys
  • NP_001337177.1:p.Glu338Lys
  • NP_001337178.1:p.Glu208Lys
  • NP_001337180.1:p.Glu5Lys
  • NP_006633.1:p.Glu306Lys
  • NC_000001.10:g.243471466G>A
  • NM_006642.3:c.916G>A
Protein change:
E208K
Links:
dbSNP: rs777002036
NCBI 1000 Genomes Browser:
rs777002036
Molecular consequence:
  • NM_001350246.1:c.13G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001350247.1:c.13G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001350248.1:c.1012G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001350249.1:c.622G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001350251.1:c.13G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_006642.5:c.916G>A - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Name:
Senior-Loken syndrome 7 (SLSN7)
Identifiers:
MONDO: MONDO:0013326; MedGen: C3150877; Orphanet: 3156; OMIM: 613615
Name:
Bardet-Biedl syndrome 16 (BBS16)
Identifiers:
MONDO: MONDO:0014444; MedGen: C3889474; Orphanet: 110; OMIM: 615993

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV000655042Invitaecriteria provided, single submitter
Uncertain significance
(Mar 3, 2017)
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

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):240-242.

PubMed [citation]
PMID:
28492532
PMCID:
PMC5632818

Details of each submission

From Invitae, SCV000655042.1

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

Description

This sequence change replaces glutamic acid with lysine at codon 306 of the SDCCAG8 protein (p.Glu306Lys). The glutamic acid residue is highly conserved and there is a small physicochemical difference between glutamic acid and lysine. This variant is present in population databases (rs777002036, ExAC 0.08%) but has not been reported in the literature in individuals with an SDCCAG8-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: "Tolerated"; PolyPhen-2: "Probably Damaging"; Align-GVGD: "Class C0"). In summary, this variant is a rare missense change with uncertain impact on protein function. Because it is found in the population at an appreciable frequency, this variant is not anticipated to cause disease. However, the available evidence is currently insufficient to prove that conclusively. Therefore, it has been classified as a Variant of Uncertain Significance.

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

Last Updated: Oct 7, 2021

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