NM_006642.5(SDCCAG8):c.1409A>G (p.Glu470Gly) AND Senior-Loken syndrome 7

Germline classification:: Likely benign (1 submission)
Last evaluated:: Jan 13, 2018
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:: RCV001099561.12

Allele description [Variation Report for NM_006642.5(SDCCAG8):c.1409A>G (p.Glu470Gly)]

NM_006642.5(SDCCAG8):c.1409A>G (p.Glu470Gly)

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.1409A>G (p.Glu470Gly)

HGVS:

NC_000001.11:g.243344267A>G
NG_027811.1:g.93263A>G
NM_001350246.2:c.506A>G
NM_001350247.2:c.506A>G
NM_001350248.2:c.1505A>G
NM_001350249.2:c.1115A>G
NM_001350251.2:c.506A>G
NM_006642.5:c.1409A>GMANE SELECT
NP_001337175.1:p.Glu169Gly
NP_001337176.1:p.Glu169Gly
NP_001337177.1:p.Glu502Gly
NP_001337178.1:p.Glu372Gly
NP_001337180.1:p.Glu169Gly
NP_006633.1:p.Glu470Gly
NC_000001.10:g.243507569A>G
NM_006642.3:c.1409A>G

Protein change:

E169G

Links:

dbSNP: rs118064970

Molecular consequence:

NM_001350246.2:c.506A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001350247.2:c.506A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001350248.2:c.1505A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001350249.2:c.1115A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001350251.2:c.506A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_006642.5:c.1409A>G - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Name:: Senior-Loken syndrome 7 (SLSN7)
Identifiers:: MONDO: MONDO:0013326; MedGen: C3150877; Orphanet: 3156; OMIM: 613615

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV001256026	Illumina Laboratory Services, Illumina	criteria provided, single submitter (ICSL Variant Classification Criteria 13 December 2019)	Likely benign (Jan 13, 2018)	germline	clinical testing	Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV001256026

Illumina Laboratory Services, Illumina

criteria provided, single submitter

(ICSL Variant Classification Criteria 13 December 2019)

Likely benign
(Jan 13, 2018)

germline

clinical testing

Citation Link

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

Details of each submission

From Illumina Laboratory Services, Illumina, SCV001256026.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	not provided

Description

This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score and internal cut-off values, a variant classified as likely benign is not then subjected to further curation. The score for this variant resulted in a classification of likely benign for this disease.

#	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: Jul 14, 2026

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