SPIC

Spi-C transcription factor, the group of ETS transcription factor family

Basic information

Region (hg38): 12:101475336-101486997

Links

ENSG00000166211 ∙ NCBI:121599 ∙ OMIM:612568 ∙ HGNC:29549 ∙ Uniprot:Q8N5J4 ∙ 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 SPIC gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SPIC 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			16	1		17
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	16	1	2

Variants in SPIC

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

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

Position	Type	Phenotype	Significance	ClinVar
12-101477559-C-G		not specified	Uncertain significance (May 23, 2023)
12-101477567-G-A		not specified	Uncertain significance (Apr 06, 2024)
12-101479599-G-A		not specified	Uncertain significance (Dec 01, 2023)
12-101479614-C-T		not specified	Likely benign (Apr 10, 2023)
12-101479645-A-G		not specified	Uncertain significance (Feb 06, 2024)
12-101479687-C-T		not specified	Uncertain significance (Mar 02, 2023)
12-101482818-A-T		not specified	Uncertain significance (Dec 28, 2022)
12-101482823-A-G		not specified	Uncertain significance (Feb 25, 2025)
12-101482858-C-A		not specified	Uncertain significance (Oct 03, 2022)
12-101482870-C-T		not specified	Uncertain significance (Dec 28, 2024)
12-101482891-G-T		not specified	Uncertain significance (Jul 05, 2023)
12-101486352-A-G		not specified	Uncertain significance (Feb 08, 2025)
12-101486372-C-T			Benign (Sep 25, 2018)
12-101486376-C-T		not specified	Uncertain significance (Feb 26, 2025)
12-101486388-T-C		not specified	Uncertain significance (Dec 09, 2024)
12-101486404-C-A		not specified	Uncertain significance (Jul 30, 2023)
12-101486510-G-A			Benign (Jul 13, 2018)
12-101486512-C-T		not specified	Uncertain significance (Nov 25, 2024)
12-101486529-A-G		not specified	Uncertain significance (Oct 03, 2022)
12-101486558-A-T		not specified	Uncertain significance (Dec 20, 2023)
12-101486611-C-G		not specified	Uncertain significance (Aug 26, 2024)
12-101486644-T-A		not specified	Uncertain significance (Apr 17, 2023)
12-101486669-G-C		not specified	Uncertain significance (Dec 09, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SPIC	protein_coding	protein_coding	ENST00000551346	5	11577

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.307	0.690	125738	0	7	125745	0.0000278

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.297	121	131	0.927	0.00000660	1639
Missense in Polyphen		16	34.945	0.45786		488
Synonymous	-0.675	56	49.9	1.12	0.00000278	438
Loss of Function	2.51	3	12.6	0.238	6.18e-7	148

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000291	0.0000291
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000353	0.0000352
Middle Eastern	0.00	0.00
South Asian	0.0000653	0.0000653
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Controls the development of red pulp macrophages required for red blood cells recycling and iron homeostasis. Transcription factor that binds to the PU-box, a purine-rich DNA sequence (5'-GAGGA[AT]-3') that can act as a lymphoid-specific enhancer. Regulates VCAM1 gene expression (By similarity). {ECO:0000250}.

Recessive Scores

• pRec: 0.108

Intolerance Scores

• loftool: 0.403
• rvis_EVS: -0.1
• rvis_percentile_EVS: 46.49

Haploinsufficiency Scores

• pHI: 0.145
• hipred: N
• hipred_score: 0.403
• ghis: 0.427

Essentials

• essential_gene_CRISPR: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.722

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Spic
• Phenotype: homeostasis/metabolism phenotype; immune system phenotype; normal 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); hematopoietic system phenotype

Gene ontology

• Biological process: blastocyst development;regulation of transcription by RNA polymerase II;cell differentiation;positive regulation of transcription by RNA polymerase II
• Cellular component: nucleus
• Molecular function: RNA polymerase II proximal promoter sequence-specific DNA binding;DNA-binding transcription factor activity, RNA polymerase II-specific;DNA-binding transcription activator activity, RNA polymerase II-specific