SDCCAG8

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

Basic information

Region (hg38): 1:243256033-243500091

Links

ENSG00000054282 ∙ NCBI:10806 ∙ OMIM:613524 ∙ HGNC:10671 ∙ Uniprot:Q86SQ7 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

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

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Bardet-Biedl syndrome 16	AR	Endocrine	Medical management of obesity with melanocortin-4 receptor (MC4R) agonist (setmelanotide) may be beneficial	Musculoskeletal; Neurologic; Ophthalmologic; Renal	20835237; 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	78	3	87
missense			227	3	1	231
nonsense	9	7				16
start loss						0
frameshift	8	5	1			14
inframe indel			5			5
splice donor/acceptor (+/-2bp)	1	12	3			16
splice region			18	18	1	37
non coding		1	13	48	19	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)
1-243256044-C-A		Senior-Loken syndrome 7 • Bardet-Biedl syndrome 16	Uncertain significance (Jan 13, 2018)
1-243256053-C-T		Senior-Loken syndrome 7 • Bardet-Biedl syndrome 16	Uncertain significance (Jan 12, 2018)
1-243256068-G-T		Senior-Loken syndrome 7 • Bardet-Biedl syndrome 16	Uncertain significance (Jan 13, 2018)
1-243256076-C-T		Bardet-Biedl syndrome 16 • Senior-Loken syndrome 7	Uncertain significance (Jan 13, 2018)
1-243256127-T-A		not specified • Bardet-Biedl syndrome 16 • Senior-Loken syndrome 7	Benign (Jul 15, 2021)
1-243256170-G-A		Bardet-Biedl syndrome 16 • Senior-Loken syndrome 7	Likely benign (Jan 13, 2018)
1-243256184-C-G		Senior-Loken syndrome 7;Bardet-Biedl syndrome 16	Uncertain significance (Jun 18, 2022)
1-243256185-C-G		Bardet-Biedl syndrome 16;Senior-Loken syndrome 7	Likely benign (Aug 27, 2020)
1-243256185-C-T		Senior-Loken syndrome 7;Bardet-Biedl syndrome 16	Likely benign (Jul 03, 2023)
1-243256187-C-T		Senior-Loken syndrome 7;Bardet-Biedl syndrome 16	Uncertain significance (Nov 28, 2021)
1-243256188-G-T		Bardet-Biedl syndrome 16;Senior-Loken syndrome 7 • SDCCAG8-related disorder	Likely benign (Nov 18, 2021)
1-243256189-G-C		Senior-Loken syndrome 7;Bardet-Biedl syndrome 16	Uncertain significance (Jun 13, 2022)
1-243256195-T-C		Bardet-Biedl syndrome 16;Senior-Loken syndrome 7	Uncertain significance (Oct 13, 2022)
1-243256201-C-T		Senior-Loken syndrome 7;Bardet-Biedl syndrome 16	Likely benign (Apr 30, 2023)
1-243256204-G-C		Senior-Loken syndrome 7;Bardet-Biedl syndrome 16	Uncertain significance (Aug 28, 2021)
1-243256210-A-T		Senior-Loken syndrome 7;Bardet-Biedl syndrome 16	Uncertain significance (Nov 27, 2020)
1-243256216-G-A		Senior-Loken syndrome 7;Bardet-Biedl syndrome 16	Uncertain significance (Oct 14, 2022)
1-243256219-C-T		Senior-Loken syndrome 7;Bardet-Biedl syndrome 16	Pathogenic (May 27, 2022)
1-243256220-A-G		SDCCAG8-related disorder	Uncertain significance (Oct 11, 2023)
1-243256221-G-A		Senior-Loken syndrome 7;Bardet-Biedl syndrome 16	Likely benign (May 24, 2023)
1-243256221-G-T		Bardet-Biedl syndrome 16;Senior-Loken syndrome 7	Uncertain significance (Apr 24, 2022)
1-243256233-T-TCTC		Senior-Loken syndrome 7;Bardet-Biedl syndrome 16	Uncertain significance (Mar 18, 2022)
1-243256236-C-T		Bardet-Biedl syndrome 16;Senior-Loken syndrome 7	Likely benign (Feb 03, 2022)
1-243256237-C-T		Inborn genetic diseases	Uncertain significance (Jan 30, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SDCCAG8	protein_coding	protein_coding	ENST00000366541	18	244075

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.18e-11	0.996	125647	0	101	125748	0.000402

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.0986	367	362	1.01	0.0000177	4747
Missense in Polyphen		104	101.66	1.023		1497
Synonymous	-0.522	145	137	1.06	0.00000730	1226
Loss of Function	2.71	25	44.5	0.562	0.00000208	541

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000978	0.000977
Ashkenazi Jewish	0.000198	0.000198
East Asian	0.00114	0.00114
Finnish	0.00	0.00
European (Non-Finnish)	0.000308	0.000308
Middle Eastern	0.00114	0.00114
South Asian	0.000425	0.000425
Other	0.000489	0.000489

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

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium

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