RANGAP1

Ran GTPase activating protein 1, the group of MicroRNA protein coding host genes

Basic information

Region (hg38): 22:41244778-41286187

Previous symbols: [ "SD" ]

Links

ENSG00000100401 ∙ NCBI:5905 ∙ OMIM:602362 ∙ HGNC:9854 ∙ Uniprot:P46060 ∙ 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 RANGAP1 gene.

• Inborn genetic diseases (19 variants)
• not provided (2 variants)
• not specified (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the RANGAP1 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					1	1
missense			17	2	1	20
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding					1	1
Total	0	0	17	2	3

Variants in RANGAP1

This is a list of pathogenic ClinVar variants found in the RANGAP1 region.

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

Position	Type	Phenotype	Significance	ClinVar
22-41246638-G-A		not specified	Uncertain significance (Mar 01, 2024)
22-41249337-C-T		not specified	Likely benign (Feb 28, 2023)
22-41249390-A-G		not specified	Uncertain significance (Nov 10, 2022)
22-41249402-G-A		not specified	Uncertain significance (Feb 15, 2023)
22-41249403-C-T		not specified	Uncertain significance (May 31, 2023)
22-41249429-A-G		not specified	Uncertain significance (Jan 23, 2024)
22-41249749-C-T		not specified	Uncertain significance (Jan 17, 2024)
22-41251045-T-C		not specified	Uncertain significance (May 30, 2023)
22-41254342-G-A		not specified	Uncertain significance (Sep 15, 2022)
22-41254348-G-A		not specified	Uncertain significance (Jul 12, 2023)
22-41254367-G-C			Benign (Sep 18, 2018)
22-41254388-C-T		not specified	Uncertain significance (Dec 21, 2023)
22-41254406-C-T		not specified	Uncertain significance (Jan 11, 2023)
22-41254460-C-T		not specified	Uncertain significance (Oct 05, 2023)
22-41254476-C-G		not specified	Likely benign (Dec 14, 2021)
22-41256091-C-T		not specified	Uncertain significance (Feb 01, 2023)
22-41256223-T-C		not specified	Uncertain significance (May 18, 2023)
22-41256224-C-T		not specified	Uncertain significance (Dec 13, 2021)
22-41256246-C-T			Benign (Sep 18, 2018)
22-41256717-C-G		not specified	Uncertain significance (Feb 06, 2024)
22-41256727-C-G		not specified	Uncertain significance (Sep 08, 2023)
22-41256749-T-C		not specified	Uncertain significance (Nov 18, 2022)
22-41258030-G-C		not specified	Uncertain significance (Jan 16, 2024)
22-41258047-G-C		not specified	Uncertain significance (Sep 29, 2023)
22-41258054-G-A		not specified	Uncertain significance (Dec 15, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
RANGAP1	protein_coding	protein_coding	ENST00000455915	15	40641

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0255	0.974	125728	0	20	125748	0.0000795

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.14	281	340	0.826	0.0000200	3792
Missense in Polyphen		52	101.55	0.51207		1195
Synonymous	-0.164	153	150	1.02	0.00000983	1190
Loss of Function	3.40	8	27.1	0.295	0.00000123	342

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000905	0.0000904
Ashkenazi Jewish	0.00	0.00
East Asian	0.000109	0.000109
Finnish	0.0000463	0.0000462
European (Non-Finnish)	0.000106	0.000105
Middle Eastern	0.000109	0.000109
South Asian	0.0000980	0.0000980
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: GTPase activator for RAN (PubMed:8146159, PubMed:8896452, PubMed:16428860). Converts cytoplasmic GTP-bound RAN to GDP-bound RAN, which is essential for RAN-mediated nuclear import and export (PubMed:8896452, PubMed:27160050). Mediates dissociation of cargo from nuclear export complexes containing XPO1, RAN and RANBP2 after nuclear export (PubMed:27160050). {ECO:0000269|PubMed:16428860, ECO:0000269|PubMed:27160050, ECO:0000269|PubMed:8146159, ECO:0000269|PubMed:8896452}.
• Pathway: RNA transport - Homo sapiens (human);Disease;Signal Transduction;role of ran in mitotic spindle regulation;cycling of ran in nucleocytoplasmic transport;Rev-mediated nuclear export of HIV RNA;Late Phase of HIV Life Cycle;HIV Life Cycle;Interactions of Rev with host cellular proteins;Host Interactions of HIV factors;HIV Infection;Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal;Amplification of signal from the kinetochores;Mitotic Spindle Checkpoint;Cell Cycle Checkpoints;Infectious disease;RHO GTPases Activate Formins;RHO GTPase Effectors;Signaling by Rho GTPases;mechanism of protein import into the nucleus;Signaling events mediated by HDAC Class II;Mitotic Prometaphase;Separation of Sister Chromatids;Mitotic Anaphase;Mitotic Metaphase and Anaphase;M Phase;Cell Cycle;Resolution of Sister Chromatid Cohesion;Cell Cycle, Mitotic;Sumoylation by RanBP2 regulates transcriptional repression;Signaling events mediated by HDAC Class I (Consensus)

Recessive Scores

• pRec: 0.205

Intolerance Scores

• loftool: 0.315
• rvis_EVS: -0.38
• rvis_percentile_EVS: 28.11

Haploinsufficiency Scores

• pHI: 0.274
• hipred: Y
• hipred_score: 0.621
• ghis: 0.575

Essentials

• essential_gene_CRISPR: E
• essential_gene_CRISPR2: E
• essential_gene_gene_trap: E
• gene_indispensability_pred: E
• gene_indispensability_score: 0.832

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Rangap1
• Phenotype: embryo 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); growth/size/body region phenotype

Gene ontology

• Biological process: signal transduction;negative regulation of protein export from nucleus;response to axon injury;activation of GTPase activity;cellular response to vasopressin
• Cellular component: kinetochore;condensed chromosome kinetochore;nuclear envelope;nuclear pore;nucleoplasm;cytoplasm;cytosol;aggresome;dendrite;nuclear membrane;intracellular membrane-bounded organelle;nuclear pore cytoplasmic filaments;perinuclear region of cytoplasm;mitotic spindle;axon cytoplasm;cytoplasmic periphery of the nuclear pore complex
• Molecular function: RNA binding;GTPase activator activity;protein binding;Ran GTPase binding;ubiquitin protein ligase binding;cadherin binding