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SDCCAG8

SHH signaling and ciliogenesis regulator SDCCAG8, the group of MicroRNA protein coding host genes

Basic information

Region (hg38): 1:243256033-243500091

Links

ENSG00000054282NCBI:10806OMIM:613524HGNC:10671Uniprot:Q86SQ7AlphaFoldGenCCjaxSfariGnomADPubmedClinVar

Phenotypes

GenCC

Source: genCC

  • Senior-Loken syndrome 7 (Definitive), mode of inheritance: AR
  • Bardet-Biedl syndrome 16 (Strong), mode of inheritance: AR
  • Bardet-Biedl syndrome 16 (Moderate), mode of inheritance: AR
  • Senior-Loken syndrome 7 (Moderate), mode of inheritance: AR
  • Senior-Loken syndrome (Supportive), mode of inheritance: AR
  • Bardet-Biedl syndrome (Supportive), mode of inheritance: AR
  • Bardet-Biedl syndrome 16 (Strong), mode of inheritance: AR
  • Senior-Loken syndrome 7 (Strong), mode of inheritance: AR

Clinical Genomic Database

Source: CGD

ConditionInheritanceIntervention CategoriesIntervention/Rationale Manifestation CategoriesReferences
Bardet-Biedl syndrome 16AREndocrineMedical management of obesity with melanocortin-4 receptor (MC4R) agonist (setmelanotide) may be beneficialMusculoskeletal; Neurologic; Ophthalmologic; Renal20835237; 22626039; 36356613
Renal transplant has been described

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the SDCCAG8 gene.

  • Senior-Loken syndrome 7;Bardet-Biedl syndrome 16 (272 variants)
  • Bardet-Biedl syndrome 16;Senior-Loken syndrome 7 (164 variants)
  • Bardet-Biedl syndrome 16 (56 variants)
  • Senior-Loken syndrome 7 (54 variants)
  • not provided (49 variants)
  • SDCCAG8-related condition (33 variants)
  • not specified (28 variants)
  • Inborn genetic diseases (23 variants)
  • Bardet-Biedl syndrome (11 variants)
  • Kidney disorder (6 variants)
  • Renal dysplasia and retinal aplasia (3 variants)
  • SDCCAG8-Related Disorders (3 variants)
  • Focal segmental glomerulosclerosis (2 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SDCCAG8 gene is commonly pathogenic or not.

In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.

Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.

Variant type Pathogenic Likely pathogenic VUS Likely benign Benign Sum
synonymous
6
clinvar
78
clinvar
3
clinvar
87
missense
227
clinvar
3
clinvar
1
clinvar
231
nonsense
9
clinvar
7
clinvar
16
start loss
0
frameshift
8
clinvar
5
clinvar
1
clinvar
14
inframe indel
5
clinvar
5
splice donor/acceptor (+/-2bp)
1
clinvar
12
clinvar
3
clinvar
16
splice region
18
18
1
37
non coding
1
clinvar
13
clinvar
48
clinvar
19
clinvar
81
Total 18 25 255 129 23

Highest pathogenic variant AF is 0.0000197

Variants in SDCCAG8

This is a list of pathogenic ClinVar variants found in the SDCCAG8 region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position Type Phenotype Significance ClinVar
1-243256043-T-C Senior-Loken syndrome 7 • Bardet-Biedl syndrome 16 Uncertain significance (Jan 13, 2018)296898
1-243256044-C-A Senior-Loken syndrome 7 • Bardet-Biedl syndrome 16 Uncertain significance (Jan 13, 2018)296899
1-243256053-C-T Senior-Loken syndrome 7 • Bardet-Biedl syndrome 16 Uncertain significance (Jan 12, 2018)296900
1-243256068-G-T Senior-Loken syndrome 7 • Bardet-Biedl syndrome 16 Uncertain significance (Jan 13, 2018)296901
1-243256076-C-T Bardet-Biedl syndrome 16 • Senior-Loken syndrome 7 Uncertain significance (Jan 13, 2018)296902
1-243256127-T-A not specified • Bardet-Biedl syndrome 16 • Senior-Loken syndrome 7 Benign (Jul 15, 2021)260005
1-243256170-G-A Bardet-Biedl syndrome 16 • Senior-Loken syndrome 7 Likely benign (Jan 13, 2018)296903
1-243256184-C-G Senior-Loken syndrome 7;Bardet-Biedl syndrome 16 Uncertain significance (Jun 18, 2022)2176103
1-243256185-C-G Bardet-Biedl syndrome 16;Senior-Loken syndrome 7 Likely benign (Aug 27, 2020)1137572
1-243256185-C-T Senior-Loken syndrome 7;Bardet-Biedl syndrome 16 Likely benign (Jul 03, 2023)1985166
1-243256187-C-T Senior-Loken syndrome 7;Bardet-Biedl syndrome 16 Uncertain significance (Nov 28, 2021)1491235
1-243256188-G-T Senior-Loken syndrome 7;Bardet-Biedl syndrome 16 • SDCCAG8-related condition Likely benign (Nov 18, 2021)1649550
1-243256189-G-C Senior-Loken syndrome 7;Bardet-Biedl syndrome 16 Uncertain significance (Jun 13, 2022)959154
1-243256195-T-C Bardet-Biedl syndrome 16;Senior-Loken syndrome 7 Uncertain significance (Oct 13, 2022)1470091
1-243256201-C-T Senior-Loken syndrome 7;Bardet-Biedl syndrome 16 Likely benign (Apr 30, 2023)2934878
1-243256204-G-C Senior-Loken syndrome 7;Bardet-Biedl syndrome 16 Uncertain significance (Aug 28, 2021)649596
1-243256210-A-T Senior-Loken syndrome 7;Bardet-Biedl syndrome 16 Uncertain significance (Nov 27, 2020)1443186
1-243256216-G-A Senior-Loken syndrome 7;Bardet-Biedl syndrome 16 Uncertain significance (Oct 14, 2022)2937967
1-243256219-C-T Senior-Loken syndrome 7;Bardet-Biedl syndrome 16 Pathogenic (May 27, 2022)1918532
1-243256220-A-G SDCCAG8-related condition Uncertain significance (Oct 11, 2023)2634742
1-243256221-G-A Senior-Loken syndrome 7;Bardet-Biedl syndrome 16 Likely benign (May 24, 2023)2930072
1-243256221-G-T Bardet-Biedl syndrome 16;Senior-Loken syndrome 7 Uncertain significance (Apr 24, 2022)1513320
1-243256233-T-TCTC Senior-Loken syndrome 7;Bardet-Biedl syndrome 16 Uncertain significance (Mar 18, 2022)2114010
1-243256236-C-T Bardet-Biedl syndrome 16;Senior-Loken syndrome 7 Likely benign (Feb 03, 2022)1148798
1-243256237-C-T Inborn genetic diseases Uncertain significance (Jan 30, 2024)3158890

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
SDCCAG8protein_codingprotein_codingENST00000366541 18244075
pLI Probability
LOF Intolerant
pRec Probability
LOF Recessive
Individuals with
no LOFs
Individuals with
Homozygous LOFs
Individuals with
Heterozygous LOFs
Defined p
1.18e-110.99612564701011257480.000402
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense-0.09863673621.010.00001774747
Missense in Polyphen104101.661.0231497
Synonymous-0.5221451371.060.000007301226
Loss of Function2.712544.50.5620.00000208541

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.0009780.000977
Ashkenazi Jewish0.0001980.000198
East Asian0.001140.00114
Finnish0.000.00
European (Non-Finnish)0.0003080.000308
Middle Eastern0.001140.00114
South Asian0.0004250.000425
Other0.0004890.000489

dbNSFP

Source: dbNSFP

Function
FUNCTION: Plays a role in the establishment of cell polarity and epithelial lumen formation (By similarity). May play a role in ciliogenesis. {ECO:0000250|UniProtKB:Q80UF4}.;
Disease
DISEASE: Bardet-Biedl syndrome 16 (BBS16) [MIM:615993]: A syndrome characterized by usually severe pigmentary retinopathy, early- onset obesity, polydactyly, hypogenitalism, renal malformation and mental retardation. Secondary features include diabetes mellitus, hypertension and congenital heart disease. Bardet-Biedl syndrome inheritance is autosomal recessive, but three mutated alleles (two at one locus, and a third at a second locus) may be required for clinical manifestation of some forms of the disease. {ECO:0000269|PubMed:20835237, ECO:0000269|PubMed:22626039}. Note=The disease is caused by mutations affecting the gene represented in this entry.;
Pathway
Regulation of PLK1 Activity at G2/M Transition;Recruitment of mitotic centrosome proteins and complexes;Loss of Nlp from mitotic centrosomes;Loss of proteins required for interphase microtubule organization from the centrosome;Centrosome maturation;AURKA Activation by TPX2;G2/M Transition;Mitotic G2-G2/M phases;Recruitment of NuMA to mitotic centrosomes;Mitotic Prometaphase;M Phase;Cell Cycle;Cell Cycle, Mitotic;Anchoring of the basal body to the plasma membrane;Cilium Assembly;Organelle biogenesis and maintenance (Consensus)

Recessive Scores

pRec
0.115

Intolerance Scores

loftool
0.879
rvis_EVS
-0.15
rvis_percentile_EVS
42.23

Haploinsufficiency Scores

pHI
0.138
hipred
N
hipred_score
0.328
ghis
0.559

Essentials

essential_gene_CRISPR
N
essential_gene_CRISPR2
N
essential_gene_gene_trap
N
gene_indispensability_pred
N
gene_indispensability_score
0.253

Gene Damage Prediction

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium

Mouse Genome Informatics

Gene name
Sdccag8
Phenotype
mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); digestive/alimentary phenotype; nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan); limbs/digits/tail phenotype; vision/eye phenotype; renal/urinary system phenotype; growth/size/body region phenotype; craniofacial phenotype; homeostasis/metabolism phenotype; cellular phenotype;

Zebrafish Information Network

Gene name
sdccag8
Affected structure
pronephric tubule
Phenotype tag
abnormal
Phenotype quality
decreased width

Gene ontology

Biological process
G2/M transition of mitotic cell cycle;neuron migration;centrosome cycle;regulation of G2/M transition of mitotic cell cycle;establishment of cell polarity;microtubule organizing center organization;tube formation;ciliary basal body-plasma membrane docking
Cellular component
centrosome;centriole;cytosol;cell-cell junction;centriolar satellite
Molecular function
protein binding