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.

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.

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						0
missense			25		1	26
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	25	0	1

Variants in SP6

This is a list of pathogenic ClinVar variants found in the SP6 region.

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

Position	Type	Phenotype	Significance	ClinVar
17-47847303-T-C		not specified	Uncertain significance (Aug 15, 2023)
17-47847322-C-T		not specified	Uncertain significance (Jan 03, 2024)
17-47847369-C-T		not specified	Uncertain significance (Oct 04, 2022)
17-47847372-G-A		not specified	Uncertain significance (Aug 16, 2021)
17-47847378-C-G		not specified	Uncertain significance (Mar 04, 2024)
17-47847421-C-G			Benign (Feb 01, 2024)
17-47847426-G-A		not specified	Uncertain significance (Jan 09, 2025)
17-47847453-C-G		not specified	Uncertain significance (Jun 17, 2024)
17-47847502-C-G		not specified	Uncertain significance (Aug 10, 2021)
17-47847595-T-A		not specified	Uncertain significance (Jul 27, 2024)
17-47847612-GC-AT		Amelogenesis imperfecta • Amelogenesis imperfecta, IIa 1K	Pathogenic (Oct 27, 2022)
17-47847612-GC-TT		Amelogenesis imperfecta, IIa 1K	Pathogenic (Oct 26, 2022)
17-47847658-T-C		not specified	Uncertain significance (Oct 20, 2023)
17-47847705-G-A		not specified	Uncertain significance (Dec 22, 2023)
17-47847751-C-T		not specified	Uncertain significance (Oct 20, 2023)
17-47847769-G-A		not specified	Uncertain significance (Mar 17, 2023)
17-47847808-C-A		not specified	Uncertain significance (Feb 09, 2025)
17-47847834-G-T		not specified	Uncertain significance (Jun 25, 2024)
17-47847865-C-T		not specified	Uncertain significance (Sep 29, 2023)
17-47847978-C-G		not specified	Uncertain significance (Jul 05, 2023)
17-47847981-G-T		not specified	Uncertain significance (Aug 02, 2021)
17-47848030-G-C		not specified	Uncertain significance (Jan 08, 2024)
17-47848135-C-T		not specified	Uncertain significance (Jan 21, 2025)
17-47848141-G-T		not specified	Uncertain significance (Sep 26, 2022)
17-47848188-A-T		not specified	Uncertain significance (May 20, 2024)

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