SPINDOC

spindlin interactor and repressor of chromatin binding

Basic information

Region (hg38): 11:63813455-63827716

Previous symbols: [ "C11orf84" ]

Links

ENSG00000168005 ∙ NCBI:144097 ∙ ∙ HGNC:25115 ∙ Uniprot:Q9BUA3 ∙ 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 SPINDOC gene.

• not provided (2 variants)

Variants pathogenicity by type

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

Variants in SPINDOC

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

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

Position	Type	Phenotype	Significance	ClinVar
11-63817856-G-T		not specified	Uncertain significance (Aug 12, 2021)
11-63818277-C-T			Likely benign (Mar 01, 2023)
11-63818529-G-A		not specified	Uncertain significance (Jul 14, 2021)
11-63818811-C-T		not specified	Uncertain significance (Nov 15, 2021)
11-63818844-C-T		not specified	Uncertain significance (Oct 06, 2021)
11-63818884-C-T			Likely benign (Aug 01, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SPINDOC	protein_coding	protein_coding	ENST00000294244	6	14331

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.991	0.00858	125687	0	6	125693	0.0000239

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.670	204	233	0.876	0.0000148	2439
Missense in Polyphen		52	81.033	0.64171		860
Synonymous	-0.568	107	99.8	1.07	0.00000712	794
Loss of Function	3.50	0	14.3	0.00	6.96e-7	163

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000616	0.0000615
Ashkenazi Jewish	0.0000995	0.0000992
East Asian	0.0000544	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.0000266	0.0000264
Middle Eastern	0.0000544	0.0000544
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Negatively regulates the transcriptional activator activity of SPIN1 via inhibition of its histone methyl-binding ability. Represses the expression of a number of SPIN1-regulated genes and the SPIN1-mediated activation of the Wnt signaling pathway. Can also inhibit the histone methyl-binding abilities of SPIN2A, SPIN2B, SPIN3 and SPIN4 (PubMed:29061846). {ECO:0000269|PubMed:29061846}.

Recessive Scores

• pRec: 0.135

Intolerance Scores

• rvis_EVS: 0.02
• rvis_percentile_EVS: 55.45

Haploinsufficiency Scores

• hipred: N
• hipred_score: 0.376
• ghis: 0.518

Essentials

• essential_gene_gene_trap: N

Mouse Genome Informatics

• Gene name: Spindoc

Gene ontology

• Biological process: negative regulation of transcription, DNA-templated
• Molecular function: protein binding