NM_006642.5(SDCCAG8):c.397G>T (p.Glu133Ter) AND multiple conditions

Germline classification:: Pathogenic (1 submission)
Last evaluated:: Jun 19, 2024
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:: RCV002932081.4

Allele description [Variation Report for NM_006642.5(SDCCAG8):c.397G>T (p.Glu133Ter)]

NM_006642.5(SDCCAG8):c.397G>T (p.Glu133Ter)

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.397G>T (p.Glu133Ter)

HGVS:

NC_000001.11:g.243274633G>T
NG_027811.1:g.23629G>T
NM_001350246.2:c.-716G>T
NM_001350247.2:c.-604G>T
NM_001350248.2:c.397G>T
NM_001350249.2:c.103G>T
NM_001350251.2:c.-977G>T
NM_006642.3:c.397G>T
NM_006642.5:c.397G>TMANE SELECT
NP_001337177.1:p.Glu133Ter
NP_001337178.1:p.Glu35Ter
NP_006633.1:p.Glu133Ter
NC_000001.10:g.243437935G>T

Protein change:

E133*

Links:

dbSNP: rs768207230

NCBI 1000 Genomes Browser:

rs768207230

Molecular consequence:

NM_001350246.2:c.-716G>T - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001350247.2:c.-604G>T - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001350251.2:c.-977G>T - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001350248.2:c.397G>T - nonsense - [Sequence Ontology: SO:0001587]
NM_001350249.2:c.103G>T - nonsense - [Sequence Ontology: SO:0001587]
NM_006642.5:c.397G>T - nonsense - [Sequence Ontology: SO:0001587]

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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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV003257198	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Pathogenic (Jun 19, 2024)	germline	clinical testing	PubMed (3) [See all records that cite these PMIDs] 20835237, 22190896, 28492532

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV003257198

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Pathogenic
(Jun 19, 2024)

germline

clinical testing

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

Help

Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	germline	unknown	not provided	not provided	not provided	not provided	not provided	clinical 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 (3)

Details of each submission

From Labcorp Genetics (formerly Invitae), Labcorp, SCV003257198.3

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (3)

Description

This sequence change creates a premature translational stop signal (p.Glu133*) 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). This variant is present in population databases (rs768207230, gnomAD 0.009%). This variant has not been reported in the literature in individuals affected with SDCCAG8-related conditions. ClinVar contains an entry for this variant (Variation ID: 2048826). For these reasons, this variant has been classified as Pathogenic.

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	unknown	not provided	not provided	not provided		not provided	not provided	not provided	not provided

Last Updated: Apr 7, 2025

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