GPRASP1

G protein-coupled receptor associated sorting protein 1, the group of Armadillo repeat containing

Basic information

Region (hg38): X:102651091-102659083

Links

ENSG00000198932 ∙ NCBI:9737 ∙ OMIM:300417 ∙ HGNC:24834 ∙ Uniprot:Q5JY77 ∙ 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 GPRASP1 gene.

• Inborn genetic diseases (30 variants)
• not provided (9 variants)
• Intellectual disability (3 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the GPRASP1 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	1	5
missense			31	4		35
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	31	8	1

Variants in GPRASP1

This is a list of pathogenic ClinVar variants found in the GPRASP1 region.

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

Position	Type	Phenotype	Significance	ClinVar
X-102653924-C-A		not specified	Uncertain significance (Feb 26, 2024)
X-102653934-G-C		not specified	Uncertain significance (Feb 26, 2024)
X-102654110-T-A			Uncertain significance (Sep 22, 2021)
X-102654136-C-T		not specified	Uncertain significance (Apr 07, 2023)
X-102654199-G-A		not specified	Uncertain significance (Apr 07, 2023)
X-102654236-CAGAG-C			Uncertain significance (Jan 23, 2024)
X-102654281-G-T		not specified	Uncertain significance (Jan 20, 2023)
X-102654284-C-T		not specified	Uncertain significance (Oct 13, 2023)
X-102654292-G-C		not specified	Uncertain significance (Nov 12, 2021)
X-102654535-G-A		not specified	Uncertain significance (Feb 27, 2023)
X-102654568-G-A		not specified	Uncertain significance (Mar 31, 2023)
X-102654650-A-G		not specified	Uncertain significance (Feb 27, 2024)
X-102654696-C-G			Likely benign (Apr 01, 2023)
X-102654729-G-T		not specified	Uncertain significance (Mar 02, 2023)
X-102654770-G-A		not specified	Uncertain significance (Mar 20, 2023)
X-102654844-G-A		not specified	Uncertain significance (Jun 05, 2023)
X-102654885-G-A			Likely benign (Oct 01, 2022)
X-102654970-A-G		not specified	Uncertain significance (Jan 29, 2024)
X-102655021-A-T		not specified	Uncertain significance (May 05, 2022)
X-102655069-A-C		not specified	Uncertain significance (Oct 12, 2021)
X-102655213-A-G		not specified	Uncertain significance (Sep 26, 2023)
X-102655271-G-C		not specified	Uncertain significance (Oct 10, 2023)
X-102655456-G-A		not specified	Uncertain significance (Mar 12, 2024)
X-102655460-C-G		not specified	Conflicting classifications of pathogenicity (Dec 01, 2022)
X-102655530-G-T		not specified	Uncertain significance (Feb 28, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
GPRASP1	protein_coding	protein_coding	ENST00000537097	1	7718

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.311	0.689	125707	12	27	125746	0.000155

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.728	454	500	0.908	0.0000347	9323
Missense in Polyphen		70	85.828	0.81559		1778
Synonymous	1.72	147	176	0.835	0.0000127	2611
Loss of Function	4.20	8	34.7	0.231	0.00000271	567

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000335	0.000306
Ashkenazi Jewish	0.00	0.00
East Asian	0.000505	0.000381
Finnish	0.0000625	0.0000462
European (Non-Finnish)	0.000270	0.000193
Middle Eastern	0.000505	0.000381
South Asian	0.000105	0.0000653
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Modulates lysosomal sorting and functional down- regulation of a variety of G-protein coupled receptors. Targets receptors for degradation in lysosomes via its interaction with BECN2. {ECO:0000269|PubMed:12142540, ECO:0000269|PubMed:15452121, ECO:0000269|PubMed:23954414}.

Intolerance Scores

• loftool: 0.810
• rvis_EVS: -0.24
• rvis_percentile_EVS: 36.28

Haploinsufficiency Scores

• pHI: 0.238
• hipred: N
• hipred_score: 0.301
• ghis: 0.562

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.611

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Gprasp1
• Phenotype: behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan)

Gene ontology

• Biological process: endosome to lysosome transport;G protein-coupled receptor catabolic process
• Cellular component: cytosol
• Molecular function: protein binding