ASCC2

activating signal cointegrator 1 complex subunit 2, the group of Activating signal cointegrator 1 complex

Basic information

Region (hg38): 22:29788609-29838304

Links

ENSG00000100325 ∙ NCBI:84164 ∙ OMIM:614216 ∙ HGNC:24103 ∙ Uniprot:Q9H1I8 ∙ 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 ASCC2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ASCC2 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			49	2		51
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	49	2	0

Variants in ASCC2

This is a list of pathogenic ClinVar variants found in the ASCC2 region.

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

Position	Type	Phenotype	Significance	ClinVar
22-29789062-C-T		not specified	Uncertain significance (Jan 30, 2024)
22-29789074-G-C		not specified	Uncertain significance (Sep 05, 2024)
22-29789083-G-A		not specified	Uncertain significance (Feb 06, 2024)
22-29789107-C-G		not specified	Uncertain significance (Oct 16, 2024)
22-29789110-T-C		not specified	Uncertain significance (Jan 27, 2022)
22-29789125-C-T		not specified	Uncertain significance (Nov 09, 2023)
22-29789143-C-T		not specified	Uncertain significance (Jan 27, 2022)
22-29790493-C-T		not specified	Uncertain significance (Aug 12, 2021)
22-29792435-T-G		not specified	Uncertain significance (Sep 22, 2023)
22-29792447-C-T		not specified	Uncertain significance (Dec 14, 2023)
22-29792527-G-A		not specified	Uncertain significance (Mar 30, 2022)
22-29793363-C-A		not specified	Uncertain significance (Aug 10, 2021)
22-29793364-G-T		not specified	Uncertain significance (Mar 07, 2024)
22-29793370-T-A		not specified	Uncertain significance (Dec 19, 2022)
22-29793406-C-T		not specified	Uncertain significance (Sep 12, 2023)
22-29793418-C-G		not specified	Uncertain significance (Sep 04, 2024)
22-29793467-G-C		not specified	Uncertain significance (Jan 09, 2024)
22-29793608-C-A		not specified	Uncertain significance (Dec 17, 2023)
22-29793635-T-C		not specified	Uncertain significance (Aug 17, 2021)
22-29800994-T-C		not specified	Likely benign (Mar 04, 2024)
22-29801010-G-A		not specified	Uncertain significance (Oct 05, 2023)
22-29801073-G-A		not specified	Uncertain significance (Nov 21, 2024)
22-29801094-G-A		not specified	Uncertain significance (Jul 25, 2023)
22-29802003-T-C		not specified	Likely benign (Jul 05, 2022)
22-29802006-C-T		not specified	Uncertain significance (Nov 17, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ASCC2	protein_coding	protein_coding	ENST00000397771	19	49675

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0310	0.969	125721	0	26	125747	0.000103

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.21	377	449	0.839	0.0000271	4982
Missense in Polyphen		73	95.056	0.76796		1006
Synonymous	1.28	167	189	0.881	0.0000130	1433
Loss of Function	4.33	11	40.9	0.269	0.00000197	468

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000181	0.000181
Ashkenazi Jewish	0.000100	0.0000992
East Asian	0.000218	0.000217
Finnish	0.0000462	0.0000462
European (Non-Finnish)	0.000106	0.000105
Middle Eastern	0.000218	0.000217
South Asian	0.0000980	0.0000980
Other	0.000163	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Plays a role in DNA damage repair as component of the ASCC complex. Recruits ASCC3 and ALKBH3 to sites of DNA damage by binding to polyubiquitinated proteins that have 'Lys-63'-linked polyubiquitin chains (PubMed:29144457). Part of the ASC-1 complex that enhances NF-kappa-B, SRF and AP1 transactivation (PubMed:12077347). {ECO:0000269|PubMed:12077347, ECO:0000269|PubMed:29144457}.
• Pathway: DNA Repair;ALKBH3 mediated reversal of alkylation damage;Reversal of alkylation damage by DNA dioxygenases;DNA Damage Reversal (Consensus)

Recessive Scores

• pRec: 0.122

Intolerance Scores

• loftool: 0.652
• rvis_EVS: 0.58
• rvis_percentile_EVS: 82.32

Haploinsufficiency Scores

• pHI: 0.150
• hipred: N
• hipred_score: 0.428
• ghis: 0.422

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.909

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Ascc2
• Phenotype: hearing/vestibular/ear phenotype; limbs/digits/tail phenotype; vision/eye phenotype; immune system 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: DNA dealkylation involved in DNA repair;regulation of transcription, DNA-templated
• Cellular component: nucleus;nucleoplasm;nuclear speck;activating signal cointegrator 1 complex