SP6

Sp6 transcription factor, the group of Sp transcription factors|Zinc fingers C2H2-type

Basic information

Region (hg38): 17:47844908-47855874

Links

ENSG00000189120

∙ NCBI:80320 ∙ OMIM:608613 ∙ HGNC:14530 ∙ Uniprot:Q3SY56 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

amelogenesis imperfecta, IIa 1K (Strong), mode of inheritance: AD

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Amelogenesis imperfecta, type IK	AD	General	Genetic knowledge may be beneficial related to issues such as selection of optimal supportive care, informed medical decision-making, prognostic considerations, and avoidance of unnecessary testing	Dental	32167558; 33652941

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the SP6 gene.

not_specified (45 variants)
Amelogenesis_imperfecta,_IIa_1K (2 variants)
not_provided (1 variants)
Amelogenesis_imperfecta (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SP6 gene is commonly pathogenic or not. These statistics are base on transcript: NM_001258248.2. Only rare variants are included in the table.

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.

Effect	PathogenicP	Likely pathogenicLP	VUSVUS	Likely benignLB	BenignB	Sum
synonymous						0
missense	2 clinvar		45 clinvar		1 clinvar	48
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	2	0	45	0	1

Loading clinvar variants...

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SP6	protein_coding	protein_coding	ENST00000536300	1	10962

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.150	0.835	125557	0	8	125565	0.0000319

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.34	169	226	0.748	0.0000127	2364
Missense in Polyphen		45	69.89	0.64387		685
Synonymous	0.827	98	109	0.899	0.00000675	801
Loss of Function	2.09	3	10.2	0.295	4.78e-7	105

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000290	0.0000290
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.0000466	0.0000462
European (Non-Finnish)	0.0000374	0.0000352
Middle Eastern	0.00	0.00
South Asian	0.0000655	0.0000653
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Function: FUNCTION: Promotes cell proliferation. {ECO:0000250}.;

Recessive Scores

pRec: 0.110

Haploinsufficiency Scores

pHI: 0.726
hipred: Y
hipred_score: 0.577
ghis: 0.542

Essentials

essential_gene_CRISPR: N
essential_gene_CRISPR2: N
essential_gene_gene_trap: N
gene_indispensability_pred: N
gene_indispensability_score: 0.210

Gene Damage Prediction

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

Mouse Genome Informatics

Gene name: Sp6
Phenotype: craniofacial phenotype; endocrine/exocrine gland phenotype; normal phenotype; integument phenotype (the observable morphological and physiological characteristics of the skin and its associated structures, such as the hair, nails, sweat glands, sebaceous glands and other secretory glands that are manifested through development and lifespan); 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); growth/size/body region phenotype; limbs/digits/tail phenotype; skeleton phenotype; respiratory system phenotype;

Gene ontology

Biological process: regulation of transcription by RNA polymerase II;regulation of odontogenesis
Cellular component: nucleus;cytosol
Molecular function: DNA-binding transcription factor activity, RNA polymerase II-specific;DNA binding;metal ion binding