NM_006642.5(SDCCAG8):c.518T>C (p.Leu173Pro) AND multiple conditions

Germline classification:: Uncertain significance (2 submissions)
Last evaluated:: Feb 17, 2022
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:: RCV000652118.8

Allele description [Variation Report for NM_006642.5(SDCCAG8):c.518T>C (p.Leu173Pro)]

NM_006642.5(SDCCAG8):c.518T>C (p.Leu173Pro)

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.518T>C (p.Leu173Pro)

HGVS:

NC_000001.11:g.243286369T>C
NG_027811.1:g.35365T>C
NM_001350246.2:c.-595T>C
NM_001350247.2:c.-483T>C
NM_001350248.2:c.518T>C
NM_001350249.2:c.224T>C
NM_001350251.2:c.-856T>C
NM_006642.5:c.518T>CMANE SELECT
NP_001337177.1:p.Leu173Pro
NP_001337178.1:p.Leu75Pro
NP_006633.1:p.Leu173Pro
NC_000001.10:g.243449671T>C
NM_006642.3:c.518T>C

Protein change:

L173P

Links:

dbSNP: rs541533278

Molecular consequence:

NM_001350246.2:c.-595T>C - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001350247.2:c.-483T>C - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001350251.2:c.-856T>C - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001350248.2:c.518T>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001350249.2:c.224T>C - missense variant - [Sequence Ontology: SO:0001583]
NM_006642.5:c.518T>C - missense variant - [Sequence Ontology: SO:0001583]

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

Recent activity

Clear Turn Off Turn On

Your browsing activity is empty.

Activity recording is turned off.

Turn recording back on

Help

Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000773986	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (Oct 27, 2021)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]
SCV000894773	Fulgent Genetics, Fulgent Genetics	criteria provided, single submitter (ACMG Guidelines, 2015)	Uncertain significance (Feb 17, 2022)	unknown	clinical testing	PubMed (1) [See all records that cite this PMID]

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000773986

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(Oct 27, 2021)

germline

clinical testing

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

SCV000894773

Fulgent Genetics, Fulgent Genetics

criteria provided, single submitter

(ACMG Guidelines, 2015)

Uncertain significance
(Feb 17, 2022)

unknown

clinical testing

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

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
not provided	unknown	unknown	not provided	not provided	not provided	not provided	not provided	clinical testing

Citations

PubMed

Sherloc: a comprehensive refinement of the ACMG-AMP variant classification criteria.

Nykamp K, Anderson M, Powers M, Garcia J, Herrera B, Ho YY, Kobayashi Y, Patil N, Thusberg J, Westbrook M; Invitae Clinical Genomics Group, Topper S.

Genet Med. 2017 Oct;19(10):1105-1117. doi: 10.1038/gim.2017.37. Epub 2017 May 11. Erratum in: Genet Med. 2020 Jan;22(1):240. doi: 10.1038/s41436-019-0624-9..

PubMed [citation]

PMID:: 28492532
PMCID:: PMC5632818

Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology.

Richards S, Aziz N, Bale S, Bick D, Das S, Gastier-Foster J, Grody WW, Hegde M, Lyon E, Spector E, Voelkerding K, Rehm HL; ACMG Laboratory Quality Assurance Committee.

Genet Med. 2015 May;17(5):405-24. doi: 10.1038/gim.2015.30. Epub 2015 Mar 5.

PubMed [citation]

PMID:: 25741868
PMCID:: PMC4544753

PMC

Richards S, Aziz N, Bale S, Bick D, Das S, Gastier-Foster J, Grody WW, Hegde M, Lyon E, Spector E, Voelkerding K, Rehm HL, ACMG Laboratory Quality Assurance Committee.

Genetics in medicine : official journal of the American College of Medical Genetics. 2015 May; 17(5): 405-24

PMC [article]

PMCID:: PMC4544753
PMID:: 25741868
DOI:: 10.1038/gim.2015.30

Details of each submission

From Labcorp Genetics (formerly Invitae), Labcorp, SCV000773986.4

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

Description

This sequence change replaces leucine, a(n) neutral and non-polar amino acid, with proline, a(n) neutral and non-polar amino acid, at codon 173 of the SDCCAG8 protein (p.Leu173Pro). This variant is present in population databases (rs541533278, gnomAD 0.01%), including at least one homozygous and/or hemizygous individual. 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: 541793). Algorithms developed to predict the effect of missense changes on protein structure and function are either unavailable or do not agree on the potential impact of this missense change (SIFT: "Deleterious"; PolyPhen-2: "Possibly Damaging"; Align-GVGD: "Class C0"). 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.

#	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

From Fulgent Genetics, Fulgent Genetics, SCV000894773.2

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

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

Last Updated: Apr 12, 2026

ClinVar

Relating variation to medicine