ARFRP1

ADP ribosylation factor related protein 1, the group of ARF GTPase family

Basic information

Region (hg38): 20:63698642-63708025

Links

ENSG00000101246

∙ NCBI:10139 ∙ OMIM:604699 ∙ HGNC:662 ∙ Uniprot:Q13795 ∙ 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 ARFRP1 gene.

not_specified (32 variants)
not_provided (1 variants)
Dyskeratosis_congenita,_autosomal_recessive_5 (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ARFRP1 gene is commonly pathogenic or not. These statistics are base on transcript: NM_001267547.3. Only rare variants are included in the table.

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.

Effect	PathogenicP	Likely pathogenicLP	VUSVUS	Likely benignLB	BenignB	Sum
synonymous					1 clinvar	1
missense			31 clinvar	1 clinvar		32
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	31	1	1

Loading clinvar variants...

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ARFRP1	protein_coding	protein_coding	ENST00000359715	7	9382

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.137	0.859	124972	0	28	125000	0.000112

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.852	103	130	0.790	0.00000854	1296
Missense in Polyphen		27	49.133	0.54953		548
Synonymous	-0.955	69	59.6	1.16	0.00000444	386
Loss of Function	2.52	4	14.3	0.280	7.77e-7	150

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.000100	0.000100
East Asian	0.0000547	0.0000544
Finnish	0.000991	0.000971
European (Non-Finnish)	0.0000357	0.0000355
Middle Eastern	0.0000547	0.0000544
South Asian	0.0000327	0.0000327
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Function: FUNCTION: Trans-Golgi-associated GTPase that regulates protein sorting. Controls the targeting of ARL1 and its effector to the trans-Golgi. Required for the lipidation of chylomicrons in the intestine and required for VLDL lipidation in the liver. {ECO:0000250|UniProtKB:Q8BXL7}.;
Pathway: Vesicle-mediated transport;Membrane Trafficking;Retrograde transport at the Trans-Golgi-Network;Intra-Golgi and retrograde Golgi-to-ER traffic (Consensus)

Recessive Scores

pRec: 0.235

Intolerance Scores

loftool: 0.247
rvis_EVS: -0.14
rvis_percentile_EVS: 43.29

Haploinsufficiency Scores

pHI: 0.120
hipred: Y
hipred_score: 0.507
ghis: 0.591

Essentials

essential_gene_CRISPR: N
essential_gene_CRISPR2: E
essential_gene_gene_trap: N
gene_indispensability_pred: E
gene_indispensability_score: 0.934

Gene Damage Prediction

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

Mouse Genome Informatics

Gene name: Arfrp1
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); embryo phenotype; cellular phenotype;

Gene ontology

Biological process: intracellular protein transport;signal transduction;gastrulation;protein localization to organelle;protein localization to Golgi apparatus;retrograde transport, endosome to Golgi;Golgi to plasma membrane protein transport
Cellular component: Golgi apparatus;trans-Golgi network;cytosol;membrane;trans-Golgi network membrane
Molecular function: GTPase activity;protein binding;GTP binding