ARID3C

AT-rich interaction domain 3C, the group of AT-rich interaction domain containing

Basic information

Region (hg38): 9:34621049-34629066

Links

ENSG00000205143 ∙ NCBI:138715 ∙ ∙ HGNC:21209 ∙ Uniprot:A6NKF2 ∙ 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 ARID3C gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ARID3C 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			24			24
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	24	0	0

Variants in ARID3C

This is a list of pathogenic ClinVar variants found in the ARID3C region.

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

Position	Type	Phenotype	Significance	ClinVar
9-34621463-G-A		not specified	Uncertain significance (Jun 23, 2021)
9-34621481-G-C		not specified	Uncertain significance (Mar 31, 2023)
9-34621499-G-A		not specified	Uncertain significance (Mar 27, 2023)
9-34621505-G-A		not specified	Uncertain significance (Oct 06, 2021)
9-34621517-C-T		not specified	Uncertain significance (Dec 20, 2023)
9-34621541-G-A		not specified	Uncertain significance (Apr 08, 2022)
9-34621544-G-A		not specified	Uncertain significance (Jun 06, 2023)
9-34622025-T-C		not specified	Uncertain significance (Apr 23, 2024)
9-34622065-T-A		not specified	Uncertain significance (Sep 26, 2022)
9-34622072-A-C		not specified	Uncertain significance (Apr 26, 2024)
9-34622510-G-T		not specified	Uncertain significance (Aug 20, 2024)
9-34623481-G-A		not specified	Uncertain significance (Oct 29, 2024)
9-34623510-C-A		not specified	Uncertain significance (Oct 09, 2024)
9-34623524-G-A		EBV-positive nodal T- and NK-cell lymphoma	Likely benign (-)
9-34623544-G-A		not specified	Uncertain significance (Nov 13, 2024)
9-34623589-A-T		not specified	Uncertain significance (Nov 07, 2024)
9-34623605-A-G		not specified	Uncertain significance (Dec 02, 2024)
9-34623607-G-A		not specified	Uncertain significance (Jun 01, 2022)
9-34623638-C-T		not specified	Uncertain significance (Nov 09, 2024)
9-34623662-G-C		not specified	Uncertain significance (May 02, 2024)
9-34623692-A-G		not specified	Uncertain significance (Apr 21, 2022)
9-34623710-T-C		not specified	Uncertain significance (Dec 18, 2023)
9-34623888-G-C		not specified	Uncertain significance (Sep 01, 2021)
9-34623913-G-A		not specified	Uncertain significance (Feb 16, 2023)
9-34624020-A-G		not specified	Uncertain significance (Dec 08, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ARID3C	protein_coding	protein_coding	ENST00000378909	7	6729

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
3.05e-9	0.170	125520	0	227	125747	0.000903

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.493	222	244	0.911	0.0000142	2589
Missense in Polyphen		58	73.875	0.78511		780
Synonymous	2.35	72	102	0.705	0.00000599	902
Loss of Function	0.374	14	15.6	0.898	7.45e-7	180

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000342	0.000331
Ashkenazi Jewish	0.00	0.00
East Asian	0.000221	0.000217
Finnish	0.00615	0.00616
European (Non-Finnish)	0.000555	0.000536
Middle Eastern	0.000221	0.000217
South Asian	0.000297	0.000294
Other	0.00180	0.00179

dbNSFP

Source: dbNSFP

Recessive Scores

• pRec: 0.0810

Intolerance Scores

• loftool: 0.876
• rvis_EVS: 0.53
• rvis_percentile_EVS: 80.82

Haploinsufficiency Scores

• pHI: 0.324
• hipred: N
• hipred_score: 0.205

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.00556

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Arid3c

Gene ontology

• Biological process: positive regulation of transcription by RNA polymerase II
• Cellular component: nucleus;cytoplasm;membrane raft
• Molecular function: RNA polymerase II regulatory region sequence-specific DNA binding;DNA-binding transcription activator activity, RNA polymerase II-specific;chromatin binding