CACTIN

cactin, spliceosome C complex subunit, the group of Spliceosomal C complex|Spliceosomal P complex

Basic information

Region (hg38): 19:3610645-3626815

Previous symbols: [ "C19orf29" ]

Links

ENSG00000105298 ∙ NCBI:58509 ∙ OMIM:618536 ∙ HGNC:29938 ∙ Uniprot:Q8WUQ7 ∙ 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 CACTIN gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CACTIN 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			26	2		28
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	26	2	0

Variants in CACTIN

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

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

Position	Type	Phenotype	Significance	ClinVar
19-3612003-G-A		not specified	Uncertain significance (Feb 10, 2022)
19-3612035-T-C		not specified	Uncertain significance (Dec 22, 2023)
19-3612067-G-C		not specified	Uncertain significance (Jul 12, 2023)
19-3612368-T-C		not specified	Uncertain significance (Jun 30, 2023)
19-3612369-T-G		not specified	Uncertain significance (Oct 05, 2022)
19-3613107-A-T		not specified	Uncertain significance (Dec 13, 2023)
19-3613294-A-G		not specified	Likely benign (Feb 02, 2022)
19-3613336-G-C		not specified	Uncertain significance (Mar 07, 2024)
19-3613479-T-A		not specified	Uncertain significance (Dec 06, 2021)
19-3613518-T-C		not specified	Uncertain significance (Sep 13, 2023)
19-3613531-C-G		not specified	Uncertain significance (Oct 14, 2023)
19-3614488-C-T		not specified	Uncertain significance (Jun 04, 2024)
19-3619089-C-G		not specified	Uncertain significance (Apr 23, 2024)
19-3619166-C-T		not specified	Uncertain significance (Nov 17, 2023)
19-3619178-C-T		not specified	Uncertain significance (Dec 06, 2021)
19-3620750-C-T		not specified	Uncertain significance (Feb 28, 2024)
19-3620754-C-T		not specified	Uncertain significance (Jun 18, 2024)
19-3623716-T-C		not specified	Uncertain significance (Feb 02, 2022)
19-3623882-G-A		not specified	Uncertain significance (May 08, 2023)
19-3623913-G-C		not specified	Uncertain significance (Nov 08, 2022)
19-3623926-C-T		not specified	Uncertain significance (Aug 15, 2023)
19-3623938-G-A		not specified	Uncertain significance (Aug 17, 2022)
19-3623942-C-A		not specified	Uncertain significance (Dec 01, 2022)
19-3623948-G-A		not specified	Uncertain significance (Jul 14, 2022)
19-3623965-C-T		not specified	Uncertain significance (Apr 23, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CACTIN	protein_coding	protein_coding	ENST00000429344	10	16175

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.00	0.0000210	124434	0	2	124436	0.00000804

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	3.20	315	521	0.605	0.0000401	4820
Missense in Polyphen		90	208.43	0.4318		1836
Synonymous	-1.37	257	231	1.11	0.0000186	1446
Loss of Function	5.31	1	34.8	0.0288	0.00000168	378

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	0.00	0.00
European (Non-Finnish)	0.00000890	0.00000887
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Involved in the regulation of innate immune response. Acts as negative regulator of Toll-like receptor and interferon- regulatory factor (IRF) signaling pathways. Contributes to the regulation of transcriptional activation of NF-kappa-B target genes in response to endogenous proinflammatory stimuli. May play a role during early embryonic development. Probably involved in pre-mRNA splicing. {ECO:0000269|PubMed:20829348}.

Intolerance Scores

• rvis_EVS: -0.75
• rvis_percentile_EVS: 13.67

Haploinsufficiency Scores

• pHI: 0.111
• hipred: Y
• hipred_score: 0.728
• ghis: 0.593

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: E
• essential_gene_gene_trap: H

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Cactin

Zebrafish Information Network

• Gene name: cactin
• Affected structure: photoreceptor outer segment layer
• Phenotype tag: abnormal
• Phenotype quality: disheveled

Gene ontology

• Biological process: mRNA splicing, via spliceosome;negative regulation of protein phosphorylation;multicellular organism development;negative regulation of lipopolysaccharide-mediated signaling pathway;negative regulation of NF-kappaB transcription factor activity;negative regulation of interferon-beta production;negative regulation of interleukin-8 production;negative regulation of tumor necrosis factor production;negative regulation of toll-like receptor signaling pathway;innate immune response;negative regulation of type I interferon-mediated signaling pathway;cellular response to lipopolysaccharide;cellular response to interleukin-1;cellular response to tumor necrosis factor
• Cellular component: nucleus;nucleoplasm;cytosol;nuclear speck;catalytic step 2 spliceosome
• Molecular function: RNA binding;protein binding