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NM_006642.5(SDCCAG8):c.420+1G>C AND multiple conditions

Germline classification:
Likely pathogenic (1 submission)
Last evaluated:
Jul 1, 2022
Review status:
1 star out of maximum of 4 stars
criteria provided, single submitter
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:
RCV002775143.3

Allele description [Variation Report for NM_006642.5(SDCCAG8):c.420+1G>C]

NM_006642.5(SDCCAG8):c.420+1G>C

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.420+1G>C
HGVS:
  • NC_000001.11:g.243274657G>C
  • NG_027811.1:g.23653G>C
  • NM_001350246.2:c.-693+1G>C
  • NM_001350247.2:c.-581+1G>C
  • NM_001350248.2:c.420+1G>C
  • NM_001350249.2:c.126+1G>C
  • NM_001350251.2:c.-954+1G>C
  • NM_006642.5:c.420+1G>CMANE SELECT
  • NC_000001.10:g.243437959G>C
Molecular consequence:
  • NM_001350246.2:c.-693+1G>C - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001350247.2:c.-581+1G>C - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001350248.2:c.420+1G>C - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001350249.2:c.126+1G>C - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001350251.2:c.-954+1G>C - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_006642.5:c.420+1G>C - splice donor variant - [Sequence Ontology: SO:0001575]

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
SCV003020122Labcorp Genetics (formerly Invitae), Labcorp
criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))
Likely pathogenic
(Jul 1, 2022)
germlineclinical testing

PubMed (4)
[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

Splicing in action: assessing disease causing sequence changes.

Baralle D, Baralle M.

J Med Genet. 2005 Oct;42(10):737-48. Review.

PubMed [citation]
PMID:
16199547
PMCID:
PMC1735933

Candidate exome capture identifies mutation of SDCCAG8 as the cause of a retinal-renal ciliopathy.

Otto EA, Hurd TW, Airik R, Chaki M, Zhou W, Stoetzel C, Patil SB, Levy S, Ghosh AK, Murga-Zamalloa CA, van Reeuwijk J, Letteboer SJ, Sang L, Giles RH, Liu Q, Coene KL, Estrada-Cuzcano A, Collin RW, McLaughlin HM, Held S, Kasanuki JM, Ramaswami G, et al.

Nat Genet. 2010 Oct;42(10):840-50. doi: 10.1038/ng.662. Epub 2010 Sep 12.

PubMed [citation]
PMID:
20835237
PMCID:
PMC2947620
See all PubMed Citations (4)

Details of each submission

From Labcorp Genetics (formerly Invitae), Labcorp, SCV003020122.2

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

Description

In summary, the currently available evidence indicates that the variant is pathogenic, but additional data are needed to prove that conclusively. Therefore, this variant has been classified as Likely Pathogenic. Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant may disrupt the consensus splice site. This variant has not been reported in the literature in individuals affected with SDCCAG8-related conditions. This variant is not present in population databases (gnomAD no frequency). This sequence change affects a donor splice site in intron 4 of the SDCCAG8 gene. It is expected to disrupt RNA splicing. Variants that disrupt the donor or acceptor splice site typically lead to a loss of protein function (PMID: 16199547), and loss-of-function variants in SDCCAG8 are known to be pathogenic (PMID: 20835237, 22190896).

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

Last Updated: Sep 29, 2024