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.

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.

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			14			14
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region			1			1
non coding			1			1
Total	0	0	15	0	1

Variants in ARFRP1

This is a list of pathogenic ClinVar variants found in the ARFRP1 region.

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

Position	Type	Phenotype	Significance	ClinVar
20-63698646-G-A		Dyskeratosis congenita, autosomal recessive 5	Uncertain significance (Jan 20, 2017)
20-63698647-T-C		Dyskeratosis congenita, autosomal recessive 5	Uncertain significance (Feb 14, 2017)
20-63700462-C-T		not specified	Uncertain significance (May 22, 2023)
20-63700468-G-A		not specified	Uncertain significance (Jun 07, 2023)
20-63700495-T-C		not specified	Uncertain significance (Jun 01, 2023)
20-63700523-C-A		not specified	Uncertain significance (Feb 13, 2023)
20-63700638-C-T		not specified	Uncertain significance (Dec 15, 2023)
20-63700644-C-T		not specified	Uncertain significance (May 20, 2024)
20-63700673-C-T			Benign (May 18, 2018)
20-63700674-G-A		not specified	Uncertain significance (Nov 08, 2022)
20-63700701-G-A		not specified	Uncertain significance (Jan 26, 2022)
20-63701840-T-C		not specified	Uncertain significance (Sep 29, 2022)
20-63701873-C-T		not specified	Uncertain significance (Oct 27, 2022)
20-63701879-G-A		not specified	Uncertain significance (Jul 13, 2021)
20-63702148-T-C		not specified	Uncertain significance (May 10, 2023)
20-63706364-C-G		not specified	Uncertain significance (Jun 02, 2024)
20-63706383-C-T		not specified	Uncertain significance (Nov 09, 2023)
20-63706410-G-C		not specified	Uncertain significance (Feb 28, 2024)
20-63706696-T-C		not specified	Uncertain significance (Oct 26, 2021)

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