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NM_006204.4(PDE6C):c.86G>A (p.Arg29Gln) AND not provided

Germline classification:
Uncertain significance (2 submissions)
Last evaluated:
Jan 4, 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:
RCV000658572.27

Allele description [Variation Report for NM_006204.4(PDE6C):c.86G>A (p.Arg29Gln)]

NM_006204.4(PDE6C):c.86G>A (p.Arg29Gln)

Gene:
PDE6C:phosphodiesterase 6C [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
10q23.33
Genomic location:
Preferred name:
NM_006204.4(PDE6C):c.86G>A (p.Arg29Gln)
HGVS:
  • NC_000010.11:g.93612811G>A
  • NG_016752.1:g.5224G>A
  • NM_006204.4:c.86G>AMANE SELECT
  • NP_006195.3:p.Arg29Gln
  • NC_000010.10:g.95372568G>A
Protein change:
R29Q
Links:
dbSNP: rs781628816
NCBI 1000 Genomes Browser:
rs781628816
Molecular consequence:
  • NM_006204.4:c.86G>A - missense variant - [Sequence Ontology: SO:0001583]
Observations:
1

Condition(s)

Synonyms:
none provided
Identifiers:
MedGen: C3661900

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV000780349CeGaT Center for Human Genetics Tuebingen
criteria provided, single submitter

(CeGaT Center For Human Genetics Tuebingen Variant Classification Criteria Version 2)
Uncertain significance
(Nov 1, 2017)
germlineclinical testing

Citation Link,

SCV002161767Labcorp Genetics (formerly Invitae), Labcorp
criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))
Uncertain significance
(Jan 4, 2024)
germlineclinical testing

PubMed (4)
[See all records that cite these PMIDs]

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineyes1not providednot providednot providednot providedclinical testing
not providedgermlineunknownnot providednot providednot providednot providednot providedclinical testing

Citations

PubMed

Homozygosity mapping reveals PDE6C mutations in patients with early-onset cone photoreceptor disorders.

Thiadens AA, den Hollander AI, Roosing S, Nabuurs SB, Zekveld-Vroon RC, Collin RW, De Baere E, Koenekoop RK, van Schooneveld MJ, Strom TM, van Lith-Verhoeven JJ, Lotery AJ, van Moll-Ramirez N, Leroy BP, van den Born LI, Hoyng CB, Cremers FP, Klaver CC.

Am J Hum Genet. 2009 Aug;85(2):240-7. doi: 10.1016/j.ajhg.2009.06.016. Epub 2009 Jul 16.

PubMed [citation]
PMID:
19615668
PMCID:
PMC2725240

Decreased catalytic activity and altered activation properties of PDE6C mutants associated with autosomal recessive achromatopsia.

Grau T, Artemyev NO, Rosenberg T, Dollfus H, Haugen OH, Cumhur Sener E, Jurklies B, Andreasson S, Kernstock C, Larsen M, Zrenner E, Wissinger B, Kohl S.

Hum Mol Genet. 2011 Feb 15;20(4):719-30. doi: 10.1093/hmg/ddq517. Epub 2010 Dec 1.

PubMed [citation]
PMID:
21127010
PMCID:
PMC3269206
See all PubMed Citations (4)

Details of each submission

From CeGaT Center for Human Genetics Tuebingen, SCV000780349.29

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not provided1not providednot providedclinical testingnot provided
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineyesnot providednot providednot provided1not providednot providednot provided

From Labcorp Genetics (formerly Invitae), Labcorp, SCV002161767.3

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (4)

Description

This sequence change replaces arginine, which is basic and polar, with glutamine, which is neutral and polar, at codon 29 of the PDE6C protein (p.Arg29Gln). This variant is present in population databases (rs781628816, gnomAD 0.003%). This variant has not been reported in the literature in individuals affected with PDE6C-related conditions. ClinVar contains an entry for this variant (Variation ID: 546648). Algorithms developed to predict the effect of missense changes on protein structure and function output the following: SIFT: "Not Available"; PolyPhen-2: "Benign"; Align-GVGD: "Not Available". The glutamine amino acid residue is found in multiple mammalian species, which suggests that this missense change does not adversely affect protein function. This variant disrupts the p.Arg29 amino acid residue in PDE6C. Other variant(s) that disrupt this residue have been determined to be pathogenic (PMID: 19615668, 21127010, 30080950). This suggests that this residue is clinically significant, and that variants that disrupt this residue are likely to be disease-causing. 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.

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

Last Updated: Oct 20, 2024