NM_006642.5(SDCCAG8):c.237T>A (p.Asp79Glu) AND multiple conditions

Clinical significance:Uncertain significance (Last evaluated: Oct 14, 2019)

Review status:1 star out of maximum of 4 stars

criteria provided, single submitter

Based on:
1 submission [Details]
Record status:
current
Accession:
RCV000532918.3

Allele description [Variation Report for NM_006642.5(SDCCAG8):c.237T>A (p.Asp79Glu)]

NM_006642.5(SDCCAG8):c.237T>A (p.Asp79Glu)

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.237T>A (p.Asp79Glu)
HGVS:
  • NC_000001.11:g.243270994T>A
  • NG_027811.1:g.19990T>A
  • NM_001350246.1:c.-876T>A
  • NM_001350247.1:c.-764T>A
  • NM_001350248.1:c.237T>A
  • NM_001350249.1:c.-58T>A
  • NM_001350251.1:c.-1137T>A
  • NM_006642.5:c.237T>AMANE SELECT
  • NP_001337177.1:p.Asp79Glu
  • NP_006633.1:p.Asp79Glu
  • NC_000001.10:g.243434296T>A
  • NM_006642.3:c.237T>A
Protein change:
D79E
Links:
dbSNP: rs146474568
NCBI 1000 Genomes Browser:
rs146474568
Molecular consequence:
  • NM_001350246.1:c.-876T>A - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
  • NM_001350247.1:c.-764T>A - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
  • NM_001350249.1:c.-58T>A - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
  • NM_001350251.1:c.-1137T>A - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
  • NM_001350248.1:c.237T>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_006642.5:c.237T>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
SCV000655039Invitaecriteria provided, single submitter
Uncertain significance
(Oct 14, 2019)
germlineclinical testing

PubMed (2)
[See all records that cite these PMIDs]

Summary from all submissions

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

Citations

PubMed

High-throughput mutation analysis in patients with a nephronophthisis-associated ciliopathy applying multiplexed barcoded array-based PCR amplification and next-generation sequencing.

Halbritter J, Diaz K, Chaki M, Porath JD, Tarrier B, Fu C, Innis JL, Allen SJ, Lyons RH, Stefanidis CJ, Omran H, Soliman NA, Otto EA.

J Med Genet. 2012 Dec;49(12):756-67. doi: 10.1136/jmedgenet-2012-100973.

PubMed [citation]
PMID:
23188109

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, SCV000655039.3

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (2)

Description

This sequence change replaces aspartic acid with glutamic acid at codon 79 of the SDCCAG8 protein (p.Asp79Glu). The aspartic acid residue is weakly conserved and there is a small physicochemical difference between aspartic acid and glutamic acid. This variant is present in population databases (rs146474568, ExAC 0.08%). This variant has been reported in an individual affected with a nephronophthisis-associated ciliopathy, however a second variant was not identified in this individual (PMID: 23188109). ClinVar contains an entry for this variant (Variation ID: 296904). Algorithms developed to predict the effect of missense changes on protein structure and function (SIFT, PolyPhen-2, Align-GVGD) all suggest that this variant is likely to be tolerated, but these predictions have not been confirmed by published functional studies and their clinical significance is uncertain. In summary, this variant has uncertain impact on SDCCAG8 function. The available evidence is currently insufficient to determine its role in disease. 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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