ARHGAP44

Rho GTPase activating protein 44, the group of AH/BAR family Rho GTPase activating proteins|N-BAR domain containing

Basic information

Region (hg38): 17:12789497-12991643

Links

ENSG00000006740 ∙ NCBI:9912 ∙ OMIM:617716 ∙ HGNC:29096 ∙ Uniprot:Q17R89 ∙ 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 ARHGAP44 gene.

• Inborn genetic diseases (32 variants)
• not provided (3 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ARHGAP44 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				2	1	3
missense			30	1		31
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region				1		1
non coding						0
Total	0	0	30	3	1

Variants in ARHGAP44

This is a list of pathogenic ClinVar variants found in the ARHGAP44 region.

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

Position	Type	Phenotype	Significance	ClinVar
17-12894940-G-A		not specified	Likely benign (Jun 01, 2023)
17-12919759-A-G		not specified	Uncertain significance (Aug 02, 2021)
17-12928961-C-T		not specified	Uncertain significance (Oct 26, 2021)
17-12928979-C-T		not specified	Uncertain significance (May 05, 2022)
17-12929020-G-A		not specified	Uncertain significance (Dec 13, 2021)
17-12952541-G-A		not specified	Uncertain significance (May 27, 2022)
17-12955972-A-G			Benign (Dec 31, 2019)
17-12956684-C-T		not specified	Uncertain significance (Feb 01, 2023)
17-12958718-G-C		not specified	Uncertain significance (Feb 17, 2022)
17-12958818-C-T		not specified	Uncertain significance (May 08, 2023)
17-12958822-G-A		not specified	Uncertain significance (Oct 26, 2022)
17-12958830-G-A		not specified	Uncertain significance (Jan 29, 2024)
17-12958839-C-T		not specified	Uncertain significance (Aug 12, 2022)
17-12973309-A-G		not specified	Uncertain significance (Aug 16, 2022)
17-12974139-C-T		not specified	Uncertain significance (Jul 11, 2023)
17-12974145-G-A		not specified	Uncertain significance (Oct 26, 2022)
17-12974186-G-A		not specified	Uncertain significance (Apr 26, 2023)
17-12974191-G-A			Likely benign (Jun 23, 2018)
17-12974204-G-C		not specified	Uncertain significance (Oct 20, 2023)
17-12974210-C-T		not specified	Uncertain significance (Jun 02, 2023)
17-12974237-C-T		not specified	Uncertain significance (Dec 19, 2022)
17-12980074-G-A			Uncertain significance (Nov 13, 2023)
17-12980121-G-T		not specified	Uncertain significance (Nov 09, 2021)
17-12980128-G-A		not specified	Uncertain significance (May 25, 2022)
17-12980171-C-T		not specified	Uncertain significance (Mar 01, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ARHGAP44	protein_coding	protein_coding	ENST00000379672	21	202105

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.00	0.000122	124628	0	10	124638	0.0000401

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.39	310	453	0.684	0.0000247	5274
Missense in Polyphen		25	93.216	0.26819		1149
Synonymous	-1.51	211	185	1.14	0.0000113	1604
Loss of Function	5.73	5	47.7	0.105	0.00000265	517

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.000107	0.0000796
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.000166	0.000165

dbNSFP

Source: dbNSFP

• Function: FUNCTION: GTPase-activating protein (GAP) that stimulates the GTPase activity of Rho-type GTPases. Thereby, controls Rho-type GTPases cycling between their active GTP-bound and inactive GDP- bound states. May act as a GAP for CDC42 and RAC1. Endosomal recycling protein which, in association with SHANK3, is involved in synaptic plasticity. Promotes GRIA1 exocytosis from recycling endosomes and spine morphological changes associated to long-term potentiation. {ECO:0000269|PubMed:11431473}.
• Pathway: Signal Transduction;Rho GTPase cycle;Signaling by Rho GTPases (Consensus)

Intolerance Scores

• rvis_EVS: -1.49
• rvis_percentile_EVS: 3.63

Haploinsufficiency Scores

• hipred: Y
• hipred_score: 0.745
• ghis: 0.669

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.114

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Arhgap44
• Phenotype: behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); 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)

Gene ontology

• Biological process: exocytosis;signal transduction;regulation of actin cytoskeleton organization;negative regulation of Rac protein signal transduction;positive regulation of GTPase activity;regulation of small GTPase mediated signal transduction;regulation of dendritic spine morphogenesis;modification of dendritic spine;neurotransmitter receptor transport, endosome to postsynaptic membrane;regulation of neurotransmitter receptor transport, endosome to postsynaptic membrane
• Cellular component: cytosol;postsynaptic density;cell junction;leading edge membrane;dendritic spine;presynaptic active zone;recycling endosome;glutamatergic synapse
• Molecular function: GTPase activator activity;protein binding;phospholipid binding;Rac GTPase binding