ASPRV1

aspartic peptidase retroviral like 1, the group of Gag like LTR retrotransposon derived genes|Peptidase family A28

Basic information

Region (hg38): 2:69960088-69961631

Links

ENSG00000244617 ∙ NCBI:151516 ∙ OMIM:611765 ∙ HGNC:26321 ∙ Uniprot:Q53RT3 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• ichthyosis, lamellar, autosomal dominant (Moderate), mode of inheritance: AD
• ichthyosis, lamellar, autosomal dominant (Strong), mode of inheritance: AD

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Ichythosis, lamellar, autosomal dominant	AD	General	Genetic knowledge may be beneficial related to issues such as selection of optimal supportive care, informed medical decision-making, prognostic considerations, and avoidance of unnecessary testing	Dermatologic	32516568

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the ASPRV1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ASPRV1 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			8	1		9
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding			3	1		4
Total	0	0	11	3	0

Variants in ASPRV1

This is a list of pathogenic ClinVar variants found in the ASPRV1 region.

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

Position	Type	Phenotype	Significance	ClinVar
2-69960688-G-A		Inborn genetic diseases	Uncertain significance (Mar 19, 2024)
2-69960749-G-T		Autosomal dominant lamellar ichthyosis	Pathogenic (Aug 26, 2020)
2-69960757-C-G		Autosomal dominant lamellar ichthyosis	Pathogenic (Aug 26, 2020)
2-69960859-G-A		Inborn genetic diseases	Uncertain significance (Jan 09, 2024)
2-69960889-T-A		Inborn genetic diseases	Uncertain significance (Apr 27, 2024)
2-69960910-G-A		Inborn genetic diseases	Likely benign (Dec 01, 2022)
2-69960923-C-A		Inborn genetic diseases	Uncertain significance (Jan 23, 2024)
2-69960957-C-T			Likely benign (Jul 01, 2022)
2-69961042-T-G		Inborn genetic diseases	Uncertain significance (May 20, 2024)
2-69961094-T-C		Autosomal dominant lamellar ichthyosis	Pathogenic (Aug 26, 2020)
2-69961168-A-T		Inborn genetic diseases	Uncertain significance (Jun 28, 2022)
2-69961232-G-A		Inborn genetic diseases	Uncertain significance (Dec 21, 2022)
2-69961291-G-A		Inborn genetic diseases	Uncertain significance (Apr 12, 2024)
2-69961346-G-A		Inborn genetic diseases	Uncertain significance (Feb 28, 2023)
2-69961349-T-C		Inborn genetic diseases	Uncertain significance (Jul 15, 2021)
2-69961355-C-T		Inborn genetic diseases	Uncertain significance (Mar 18, 2024)
2-69961403-G-A		Inborn genetic diseases	Uncertain significance (Jun 11, 2024)
2-69961433-C-G		Inborn genetic diseases	Uncertain significance (Mar 01, 2023)
2-69961439-T-C		Inborn genetic diseases	Likely benign (Jan 26, 2022)
2-69961507-G-A		Inborn genetic diseases	Uncertain significance (May 24, 2024)
2-69961562-C-T		Inborn genetic diseases	Uncertain significance (Aug 26, 2022)
2-69961588-G-A		Inborn genetic diseases	Uncertain significance (Jun 13, 2024)
2-69961594-G-A		Malignant tumor of prostate • Inborn genetic diseases	Uncertain significance (Nov 29, 2023)
2-69961597-T-A		Inborn genetic diseases	Uncertain significance (Oct 14, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ASPRV1	protein_coding	protein_coding	ENST00000320256	1	2172

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00878	0.816	0	0	0	0	0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.130	192	197	0.974	0.0000110	2229
Missense in Polyphen		54	66.742	0.80909		831
Synonymous	-1.26	106	90.8	1.17	0.00000551	738
Loss of Function	1.07	4	7.07	0.566	3.68e-7	80

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)	0.00	0.00
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Recessive Scores

• pRec: 0.105

Intolerance Scores

• loftool: 0.392
• rvis_EVS: -0.25
• rvis_percentile_EVS: 36.07

Haploinsufficiency Scores

• pHI: 0.183
• hipred: N
• hipred_score: 0.146
• ghis: 0.522

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.0283

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Asprv1
• Phenotype: integument phenotype (the observable morphological and physiological characteristics of the skin and its associated structures, such as the hair, nails, sweat glands, sebaceous glands and other secretory glands that are manifested through development and lifespan)

Gene ontology

• Biological process: protein processing;skin development
• Cellular component: integral component of membrane
• Molecular function: aspartic-type endopeptidase activity