SP9

Sp9 transcription factor, the group of Zinc fingers C2H2-type|Sp transcription factors

Basic information

Region (hg38): 2:174334954-174338500

Links

ENSG00000217236 ∙ NCBI:100131390 ∙ ∙ HGNC:30690 ∙ Uniprot:P0CG40 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the SP9 gene.

• Hypotonia;Epileptic encephalopathy;EEG abnormality;Intellectual disability (1 variants)
• SP9-associated disorder (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SP9 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				2		2
missense	1		17			18
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	1	0	17	2	0

Variants in SP9

This is a list of pathogenic ClinVar variants found in the SP9 region.

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

Position	Type	Phenotype	Significance	ClinVar
2-174336114-C-T		not specified	Uncertain significance (May 30, 2024)
2-174336271-C-A		not specified	Uncertain significance (Dec 10, 2024)
2-174336273-T-C		not specified	Uncertain significance (Nov 11, 2024)
2-174336293-A-T		not specified	Uncertain significance (Jul 13, 2021)
2-174336299-G-A		not specified	Uncertain significance (Jun 27, 2023)
2-174336321-C-A		not specified	Uncertain significance (Oct 26, 2022)
2-174336321-C-T		not specified	Uncertain significance (May 17, 2023)
2-174336327-G-T		not specified	Uncertain significance (Oct 26, 2024)
2-174336371-C-T		not specified	Uncertain significance (Sep 29, 2023)
2-174336404-G-A		not specified	Uncertain significance (Jun 07, 2024)
2-174336524-C-A		not specified	Uncertain significance (Jun 10, 2024)
2-174336553-G-A			Likely benign (Jul 01, 2022)
2-174336803-T-G		not specified	Uncertain significance (Oct 29, 2024)
2-174336804-C-A		not specified	Uncertain significance (Mar 30, 2024)
2-174336809-G-A		not specified	Uncertain significance (Jan 10, 2023)
2-174336830-T-G		not specified	Uncertain significance (Aug 17, 2021)
2-174336831-C-A		not specified	Uncertain significance (Aug 17, 2021)
2-174336836-A-G		not specified	Uncertain significance (Mar 30, 2024)
2-174336859-C-G		not specified	Uncertain significance (Nov 09, 2024)
2-174336887-T-A		not specified	Uncertain significance (Mar 30, 2024)
2-174336899-G-A		not specified	Uncertain significance (Apr 04, 2023)
2-174336905-G-T		not specified	Uncertain significance (Nov 20, 2024)
2-174336954-C-G		not specified	Uncertain significance (Mar 30, 2024)
2-174336957-C-G		not specified	Uncertain significance (Mar 30, 2024)
2-174336965-A-G		not specified	Uncertain significance (Mar 30, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SP9	protein_coding	protein_coding	ENST00000394967	2	3547

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.940	0.0597	0	0	0	0	0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.26	107	196	0.545	0.00000936	3026
Missense in Polyphen		22	44.859	0.49042		494
Synonymous	0.185	86	88.2	0.975	0.00000472	1051
Loss of Function	2.77	0	8.92	0.00	3.86e-7	121

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.00	0.00
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Transcription factor which plays a key role in limb development. Positively regulates FGF8 expression in the apical ectodermal ridge (AER) and contributes to limb outgrowth in embryos (By similarity). {ECO:0000250}.

Haploinsufficiency Scores

• hipred: Y
• hipred_score: 0.580
• ghis: 0.534

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.471

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Sp9
• 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); 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); behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); cellular phenotype

Gene ontology

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