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NM_006642.5(SDCCAG8):c.1420del (p.Glu474fs) AND multiple conditions

Germline classification:
Pathogenic/Likely pathogenic (2 submissions)
Last evaluated:
Jan 12, 2023
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:
RCV001056393.6

Allele description [Variation Report for NM_006642.5(SDCCAG8):c.1420del (p.Glu474fs)]

NM_006642.5(SDCCAG8):c.1420del (p.Glu474fs)

Gene:
SDCCAG8:SHH signaling and ciliogenesis regulator SDCCAG8 [Gene - OMIM - HGNC]
Variant type:
Deletion
Cytogenetic location:
1q43
Genomic location:
Preferred name:
NM_006642.5(SDCCAG8):c.1420del (p.Glu474fs)
HGVS:
  • NC_000001.11:g.243344278del
  • NG_027811.1:g.93274del
  • NM_001350246.2:c.517del
  • NM_001350247.2:c.517del
  • NM_001350248.2:c.1516del
  • NM_001350249.2:c.1126del
  • NM_001350251.2:c.517del
  • NM_006642.5:c.1420delMANE SELECT
  • NP_001337175.1:p.Glu173fs
  • NP_001337176.1:p.Glu173fs
  • NP_001337177.1:p.Glu506fs
  • NP_001337178.1:p.Glu376fs
  • NP_001337180.1:p.Glu173fs
  • NP_006633.1:p.Glu474fs
  • NC_000001.10:g.243507579del
  • NC_000001.10:g.243507580del
  • NM_006642.3:c.1420del
  • NM_006642.3:c.1420delG
Protein change:
E173fs
Links:
OMIM: 613524.0001; dbSNP: rs397515335
NCBI 1000 Genomes Browser:
rs397515335
Molecular consequence:
  • NM_001350246.2:c.517del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001350247.2:c.517del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001350248.2:c.1516del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001350249.2:c.1126del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001350251.2:c.517del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_006642.5:c.1420del - frameshift variant - [Sequence Ontology: SO:0001589]

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

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV001220834Invitae
criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))		Pathogenic
(Jan 12, 2023) 		germlineclinical testing

PubMed (3)
[See all records that cite these PMIDs]

SCV002811456Fulgent Genetics, Fulgent Genetics
criteria provided, single submitter

(ACMG Guidelines, 2015)		Likely pathogenic
(Dec 4, 2021) 		unknownclinical testing

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

Help

Summary from all submissions

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

Citations

PubMed

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

Mutations in SDCCAG8/NPHP10 Cause Bardet-Biedl Syndrome and Are Associated with Penetrant Renal Disease and Absent Polydactyly.

Schaefer E, Zaloszyc A, Lauer J, Durand M, Stutzmann F, Perdomo-Trujillo Y, Redin C, Bennouna Greene V, Toutain A, Perrin L, Gérard M, Caillard S, Bei X, Lewis RA, Christmann D, Letsch J, Kribs M, Mutter C, Muller J, Stoetzel C, Fischbach M, Marion V, et al.

Mol Syndromol. 2011 Sep;1(6):273-281. Epub 2011 Sep 14.

PubMed [citation]
PMID:
22190896
PMCID:
PMC3214956
See all PubMed Citations (4)

Details of each submission

From Invitae, SCV001220834.5

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (3)

Description

This premature translational stop signal has been observed in individual(s) with Senior-Loken syndrome (PMID: 20835237). For these reasons, this variant has been classified as Pathogenic. ClinVar contains an entry for this variant (Variation ID: 57). This variant is present in population databases (rs770467138, gnomAD 0.02%). This sequence change creates a premature translational stop signal (p.Glu474Serfs*20) in the SDCCAG8 gene. It is expected to result in an absent or disrupted protein product. 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

From Fulgent Genetics, Fulgent Genetics, SCV002811456.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (1)
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1unknownunknownnot providednot providednot providednot providednot providednot providednot provided

Last Updated: Mar 5, 2024