RUNDC1

RUN domain containing 1

Basic information

Region (hg38): 17:42980564-42995142

Links

ENSG00000198863 ∙ NCBI:146923 ∙ OMIM:619250 ∙ HGNC:25418 ∙ Uniprot:Q96C34 ∙ 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 RUNDC1 gene.

• Inborn genetic diseases (23 variants)
• not provided (3 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the RUNDC1 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				3		3
missense			22	1		23
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	22	4	0

Variants in RUNDC1

This is a list of pathogenic ClinVar variants found in the RUNDC1 region.

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

Position	Type	Phenotype	Significance	ClinVar
17-42980593-C-T		not specified	Uncertain significance (Nov 09, 2021)
17-42980611-C-T		not specified	Uncertain significance (Jun 24, 2022)
17-42980627-T-C			Likely benign (Mar 01, 2022)
17-42980645-C-A		not specified	Uncertain significance (Oct 26, 2022)
17-42980717-G-A			Likely benign (Mar 01, 2022)
17-42980728-C-T		not specified	Uncertain significance (Dec 28, 2023)
17-42980791-C-T		not specified	Uncertain significance (May 09, 2023)
17-42980809-G-A		not specified	Uncertain significance (Nov 07, 2022)
17-42980892-T-C		not specified	Uncertain significance (Oct 26, 2021)
17-42987262-C-G		not specified	Uncertain significance (Jul 25, 2023)
17-42987274-G-A		not specified	Uncertain significance (Sep 26, 2023)
17-42987313-A-C		not specified	Uncertain significance (Feb 16, 2023)
17-42987326-A-C		not specified	Uncertain significance (Dec 19, 2022)
17-42987413-G-A		not specified	Uncertain significance (Jan 11, 2023)
17-42989426-G-A		not specified	Uncertain significance (Apr 05, 2023)
17-42989509-G-C		not specified	Uncertain significance (Dec 17, 2023)
17-42989530-T-G		not specified	Uncertain significance (Dec 20, 2023)
17-42990322-G-A		not specified	Uncertain significance (Jul 21, 2021)
17-42990326-G-C		Malignant tumor of prostate	Uncertain significance (-)
17-42990352-C-T		not specified	Uncertain significance (Aug 10, 2023)
17-42990416-C-T		not specified	Uncertain significance (Mar 31, 2023)
17-42990417-G-A			Likely benign (Mar 01, 2023)
17-42990856-G-A		not specified	Uncertain significance (Nov 01, 2022)
17-42990884-C-T		not specified	Uncertain significance (Dec 28, 2023)
17-42990902-G-A		not specified	Uncertain significance (Jul 05, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
RUNDC1	protein_coding	protein_coding	ENST00000361677	5	13126

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00237	0.995	125723	0	25	125748	0.0000994

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.13	273	331	0.825	0.0000182	3908
Missense in Polyphen		90	129.47	0.69515		1566
Synonymous	0.870	128	141	0.907	0.00000772	1302
Loss of Function	2.58	8	20.7	0.387	0.00000105	241

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000424	0.000423
Ashkenazi Jewish	0.000696	0.000695
East Asian	0.0000544	0.0000544
Finnish	0.0000462	0.0000462
European (Non-Finnish)	0.0000358	0.0000352
Middle Eastern	0.0000544	0.0000544
South Asian	0.0000655	0.0000653
Other	0.000173	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May play a role as p53/TP53 inhibitor and thus may have oncogenic activity. {ECO:0000269|PubMed:16929179}.

Intolerance Scores

• rvis_EVS: -0.56
• rvis_percentile_EVS: 19.54

Haploinsufficiency Scores

• pHI: 0.185
• hipred: N
• hipred_score: 0.476
• ghis: 0.549

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.184

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Rundc1
• Phenotype: muscle 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); normal phenotype; cardiovascular system phenotype (the observable morphological and physiological characteristics of the mammalian heart, blood vessels, or circulatory system that are manifested through development and lifespan); vision/eye phenotype; nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan); skeleton phenotype; liver/biliary system phenotype

Gene ontology

• Biological process: intracellular protein transport;activation of GTPase activity
• Cellular component: cell
• Molecular function: GTPase activator activity;Rab GTPase binding