GPRASP2

G protein-coupled receptor associated sorting protein 2, the group of Armadillo repeat containing

Basic information

Region (hg38): X:102712445-102717733

Links

ENSG00000158301 ∙ NCBI:114928 ∙ OMIM:300969 ∙ HGNC:25169 ∙ Uniprot:Q96D09 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• X-linked external auditory canal atresia-dilated internal auditory canal-facial dysmorphism syndrome (Supportive), mode of inheritance: XL
• X-linked external auditory canal atresia-dilated internal auditory canal-facial dysmorphism syndrome (Limited), mode of inheritance: Unknown

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Deafness, X-linked, 7	XL	Audiologic/Otolaryngologic	Early recognition and treatment of hearing impairment may improve outcomes, including speech and language development	Audiologic/Otolaryngologic; Craniofacial	28096187

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the GPRASP2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the GPRASP2 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				8	1	9
missense		1	31	5	3	40
nonsense						0
start loss						0
frameshift						0
inframe indel					1	1
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding				1	3	4
Total	0	1	31	14	8

Variants in GPRASP2

This is a list of pathogenic ClinVar variants found in the GPRASP2 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-102714234-A-G			Benign (May 12, 2021)
X-102714835-G-A			Benign (May 20, 2021)
X-102714903-G-C		not specified	Uncertain significance (Feb 06, 2024)
X-102714932-G-C		GPRASP2-related disorder • not specified	Uncertain significance (Feb 17, 2022)
X-102714939-G-A		not specified	Uncertain significance (Oct 16, 2023)
X-102715009-G-C		GPRASP2-related disorder • not specified	Uncertain significance (May 05, 2022)
X-102715045-C-T		not specified	Uncertain significance (May 13, 2024)
X-102715080-G-A		not specified	Uncertain significance (May 30, 2024)
X-102715113-G-T		not specified	Uncertain significance (Jun 29, 2023)
X-102715124-ACCCAAAACGGAGGCTCAAGGAATCACAGGGGCCAGG-A		GPRASP2-related disorder	Uncertain significance (Apr 29, 2024)
X-102715133-G-A		GPRASP2-related disorder	Likely benign (Mar 27, 2019)
X-102715156-C-T		not specified	Uncertain significance (Sep 13, 2023)
X-102715165-A-G		not specified	Uncertain significance (May 18, 2022)
X-102715176-A-T		not specified	Uncertain significance (Sep 27, 2022)
X-102715195-G-A		GPRASP2-related disorder	Likely benign (Oct 25, 2021)
X-102715243-AGGCCCAGGCATG-A			Benign (Apr 04, 2018)
X-102715310-G-T		not specified	Uncertain significance (Jan 10, 2023)
X-102715373-C-T		GPRASP2-related disorder	Likely benign (Oct 02, 2019)
X-102715388-A-C			Benign (May 05, 2021)
X-102715454-G-C		GPRASP2-related disorder	Likely benign (Sep 22, 2023)
X-102715567-C-T		GPRASP2-related disorder	Benign (Aug 10, 2022)
X-102715657-A-G		not specified	Uncertain significance (Dec 20, 2023)
X-102715671-T-C		not specified	Uncertain significance (May 13, 2024)
X-102715730-G-A		GPRASP2-related disorder	Likely benign (Mar 08, 2019)
X-102715734-A-G		GPRASP2-related disorder	Benign (Dec 31, 2019)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
GPRASP2	protein_coding	protein_coding	ENST00000543253	1	6504

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.988	0.0125	125734	0	8	125742	0.0000318

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.713	270	305	0.885	0.0000217	5552
Missense in Polyphen		43	68.962	0.62353		1392
Synonymous	1.17	99	115	0.861	0.00000859	1642
Loss of Function	3.67	1	17.6	0.0567	0.00000138	309

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000760	0.0000615
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.0000626	0.0000462
European (Non-Finnish)	0.0000613	0.0000440
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.000221	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May play a role in regulation of a variety of G-protein coupled receptors. {ECO:0000269|PubMed:15086532}.

Recessive Scores

• pRec: 0.0850

Intolerance Scores

• loftool: 0.656
• rvis_EVS: 0.29
• rvis_percentile_EVS: 71.5

Haploinsufficiency Scores

• pHI: 0.0589
• hipred: N
• hipred_score: 0.357
• ghis: 0.526

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.000130

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Gprasp2

Gene ontology

• Cellular component: cytoplasm
• Molecular function: amyloid-beta binding;protein binding