RUNDC3A

RUN domain containing 3A

Basic information

Region (hg38): 17:44308413-44318670

Links

ENSG00000108309 ∙ NCBI:10900 ∙ OMIM:605448 ∙ HGNC:16984 ∙ Uniprot:Q59EK9 ∙ 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 RUNDC3A gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the RUNDC3A 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			13		1	14
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	13	0	1

Variants in RUNDC3A

This is a list of pathogenic ClinVar variants found in the RUNDC3A region.

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

Position	Type	Phenotype	Significance	ClinVar
17-44312636-C-T		not specified	Uncertain significance (Dec 08, 2021)
17-44312686-C-T		not specified	Uncertain significance (Aug 10, 2021)
17-44313164-A-T		not specified	Uncertain significance (Jun 24, 2022)
17-44313436-G-T		not specified	Uncertain significance (Jun 10, 2024)
17-44313485-G-A		not specified	Uncertain significance (Oct 29, 2021)
17-44314799-A-C		not specified	Uncertain significance (Jan 06, 2023)
17-44315295-A-G		not specified	Uncertain significance (Feb 23, 2023)
17-44315584-G-C		not specified	Uncertain significance (Jul 26, 2022)
17-44315585-T-A		not specified	Uncertain significance (Nov 28, 2023)
17-44316386-A-T		not specified	Uncertain significance (Mar 21, 2024)
17-44316444-C-T		not specified	Uncertain significance (Jun 19, 2024)
17-44316467-T-C		not specified	Uncertain significance (Jan 23, 2023)
17-44316474-G-A		not specified	Uncertain significance (Jul 14, 2021)
17-44316493-G-C		not specified	Uncertain significance (May 17, 2023)
17-44316631-G-A			Benign (Aug 01, 2023)
17-44318168-C-T		not specified	Uncertain significance (Dec 19, 2023)
17-44318222-C-T		not specified	Uncertain significance (Oct 20, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
RUNDC3A	protein_coding	protein_coding	ENST00000426726	11	10259

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.636	0.364	124636	0	4	124640	0.0000160

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.69	127	246	0.517	0.0000133	2865
Missense in Polyphen		33	88.19	0.37419		924
Synonymous	0.924	94	106	0.886	0.00000592	883
Loss of Function	3.40	4	20.7	0.193	8.81e-7	270

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000290	0.0000290
Ashkenazi Jewish	0.0000995	0.0000994
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000178	0.0000177
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May act as an effector of RAP2A in neuronal cells. {ECO:0000250}.

Recessive Scores

• pRec: 0.105

Intolerance Scores

• loftool: 0.479
• rvis_EVS: -0.32
• rvis_percentile_EVS: 31.46

Haploinsufficiency Scores

• pHI: 0.333
• hipred: Y
• hipred_score: 0.789
• ghis: 0.605

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.718

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Rundc3a

Gene ontology

• Biological process: small GTPase mediated signal transduction;positive regulation of cGMP-mediated signaling;regulation of catalytic activity
• Cellular component: cytosol;plasma membrane
• Molecular function: protein binding;GTPase regulator activity