ARHGAP45

Rho GTPase activating protein 45, the group of AH/BAR family Rho GTPase activating proteins|F-BAR domain containing |Minor histocompatibility antigens

Basic information

Region (hg38): 19:1065923-1086628

Previous symbols: [ "HMHA1" ]

Links

ENSG00000180448 ∙ NCBI:23526 ∙ OMIM:601155 ∙ HGNC:17102 ∙ Uniprot:Q92619 ∙ 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 ARHGAP45 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ARHGAP45 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				4	4	8
missense			9	3	3	15
nonsense						0
start loss						0
frameshift						0
inframe indel					1	1
splice donor/acceptor (+/-2bp)						0
splice region					1	1
non coding					1	1
Total	0	0	9	7	9

Variants in ARHGAP45

This is a list of pathogenic ClinVar variants found in the ARHGAP45 region.

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

Position	Type	Phenotype	Significance	ClinVar
19-1068453-G-A		not specified	Uncertain significance (Aug 13, 2021)
19-1068473-C-T			Likely benign (Apr 24, 2018)
19-1068652-C-T		not specified	Uncertain significance (Sep 09, 2021)
19-1068735-T-C			Benign (Dec 30, 2020)
19-1068739-G-A			Benign (Dec 30, 2020)
19-1071313-C-T			Benign (Apr 10, 2019)
19-1073566-C-T		not specified	Uncertain significance (Sep 01, 2021)
19-1074853-G-A		not specified	Uncertain significance (Jun 21, 2021)
19-1077935-C-T		not specified	Uncertain significance (Aug 02, 2021)
19-1077948-C-T			Benign (Nov 15, 2018)
19-1077975-C-T		not specified	Likely benign (Sep 27, 2021)
19-1080114-G-A		not specified	Uncertain significance (Jun 23, 2021)
19-1081651-C-T			Likely benign (Oct 01, 2022)
19-1081859-G-A			Benign (Apr 04, 2018)
19-1082836-G-A			Benign (Dec 31, 2019)
19-1082989-T-G			Likely benign (Oct 01, 2022)
19-1083231-G-A		not specified	Uncertain significance (Jul 09, 2021)
19-1083343-C-G		not specified	Uncertain significance (Aug 10, 2021)
19-1084315-G-C			Benign (Dec 31, 2019)
19-1084322-G-C			Likely benign (Dec 31, 2019)
19-1084337-G-A			Likely benign (Dec 31, 2019)
19-1085691-G-A			Benign (Dec 31, 2019)
19-1085846-A-AGGACGGGGACGG			Benign (Apr 04, 2018)
19-1085857-G-A		not specified	Uncertain significance (Jun 11, 2021)
19-1085864-A-G			Benign (Dec 31, 2019)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ARHGAP45	protein_coding	protein_coding	ENST00000539243	23	20706

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.223	0.777	125693	0	45	125738	0.000179

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.07	605	766	0.790	0.0000551	7312
Missense in Polyphen		90	183.55	0.49033		1825
Synonymous	-1.34	390	358	1.09	0.0000291	2331
Loss of Function	5.07	12	51.1	0.235	0.00000246	583

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000156	0.000154
Ashkenazi Jewish	0.00	0.00
East Asian	0.00140	0.00136
Finnish	0.0000463	0.0000462
European (Non-Finnish)	0.000109	0.000106
Middle Eastern	0.00140	0.00136
South Asian	0.000103	0.0000980
Other	0.000169	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Contains a GTPase activator for the Rho-type GTPases (RhoGAP) domain that would be able to negatively regulate the actin cytoskeleton as well as cell spreading. However, also contains N-terminally a BAR-domin which is able to play an autoinhibitory effect on this RhoGAP activity. {ECO:0000269|PubMed:24086303}.
• Pathway: Neutrophil degranulation;Signal Transduction;Innate Immune System;Immune System;Rho GTPase cycle;Signaling by Rho GTPases (Consensus)

Recessive Scores

• pRec: 0.128

Intolerance Scores

• rvis_EVS: 0.01
• rvis_percentile_EVS: 54.18

Haploinsufficiency Scores

• pHI: 0.394
• hipred: Y
• hipred_score: 0.733
• ghis: 0.503

Essentials

• essential_gene_gene_trap: N

Mouse Genome Informatics

• Gene name: Arhgap45

Gene ontology

• Biological process: intracellular signal transduction;neutrophil degranulation;positive regulation of GTPase activity;regulation of small GTPase mediated signal transduction
• Cellular component: extracellular region;cytosol;membrane;ruffle membrane;secretory granule lumen;azurophil granule lumen
• Molecular function: GTPase activator activity;protein binding;metal ion binding