ARID3C

protein-coding

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

Gene summary

This gene is a member of the ARID (AT-rich interaction domain) family of proteins. The ARID domain is a helix-turn-helix motif-based DNA-binding domain. ARID family members have roles in embryonic patterning, cell lineage gene regulation, cell cycle control, transcriptional regulation and possibly in chromatin structure modification. [provided by RefSeq, Jul 2008]

MANE transcript

NM_001017363.4

Inheritance

—

ClinVar variants

U:71B:1

Top phenotype

EBV-positive nodal T- and NK-cell lymphoma

gnomAD constraint

pLI —, LoF o/e 0.9

Max pathogenic AF

—

Genomic locus

chr9:34,621,049-34,629,066

External References & Databases

Ensembl (ENSG00000205143)

Transcript & Mutation Effects

hg38 • Region Span ~8.0 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to ARID3C variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 71

EBV-positive nodal T- and NK-cell lymphomaTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_001017363.4. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous						0
missense			71 clinvar	1 clinvar		72
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	71	1	0	72

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 9 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_001017363.4	RefSeq	NP_001017363.1	7	MANE Select
ENST00000378909.4	Ensembl	ENSP00000368189.2	7	MANE Select
NM_001371945.2	RefSeq	NP_001358874.1	6	Standard
ENST00000692051.1	Ensembl	ENSP00000510553.1	5	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

positive regulation of transcription by RNA polymerase II

Molecular Function

RNA polymerase II regulatory region sequence-specific DNA binding
DNA-binding transcription activator activity, RNA polymerase II-specific
chromatin binding

Cellular Component

nucleus
cytoplasm
membrane raft

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000378909
Coding exons: 7
Length: 6729
Individuals with no LoFs: 125520
Homozygous LoFs: 0
Heterozygous LoFs: 227
Defined: 125747
p: 0.000903

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.493	222	244	0.911	0.0000142	2589
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00013	0.00012	rare
Latino/Admixed American	0.00021	0.00020	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0.00022	0.00022	rare
Finnish	0.0061	0.0062	notable
European (Non-Finnish)	0.00055	0.00054	rare
South Asian	0.00030	0.00029	rare
Other	0.0018	0.0018	notable

dbNSFP Gene Annotations

Source: dbNSFP

Recessive Scores

pRec: 0.0810

Intolerance Scores

LoFtool: 0.876
RVIS EVS: 0.53
RVIS percentile EVS: 80.82

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.00556

Gene Damage Prediction

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