PRAP1

proline rich acidic protein 1

Basic information

Region (hg38): 10:133347368-133352683

Links

ENSG00000165828 ∙ NCBI:118471 ∙ OMIM:609776 ∙ HGNC:23304 ∙ Uniprot:Q96NZ9 ∙ 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 PRAP1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PRAP1 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						0
missense			14			14
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	14	0	0

Variants in PRAP1

This is a list of pathogenic ClinVar variants found in the PRAP1 region.

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

Position	Type	Phenotype	Significance	ClinVar
10-133351429-G-A		not specified	Uncertain significance (Oct 29, 2024)
10-133352011-T-C		not specified	Uncertain significance (Sep 04, 2024)
10-133352017-G-A		not specified	Uncertain significance (Oct 26, 2021)
10-133352021-G-A		not specified	Uncertain significance (Aug 02, 2021)
10-133352036-C-G		not specified	Uncertain significance (May 24, 2024)
10-133352086-C-G		not specified	Uncertain significance (Dec 06, 2021)
10-133352126-G-T		not specified	Uncertain significance (May 23, 2024)
10-133352275-C-A		not specified	Uncertain significance (Jan 19, 2024)
10-133352285-C-T		not specified	Uncertain significance (Jul 05, 2024)
10-133352306-G-C		not specified	Uncertain significance (Nov 07, 2022)
10-133352309-C-A		not specified	Uncertain significance (May 20, 2024)
10-133352328-C-G		not specified	Uncertain significance (Jun 03, 2024)
10-133352351-G-A		not specified	Uncertain significance (Mar 01, 2024)
10-133352358-G-A		not specified	Uncertain significance (Feb 13, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PRAP1	protein_coding	protein_coding	ENST00000433452	5	5538

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0325	0.830	125601	0	6	125607	0.0000239

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.378	78	88.0	0.887	0.00000476	971
Missense in Polyphen		22	22.589	0.97392		244
Synonymous	-0.125	42	41.0	1.02	0.00000268	300
Loss of Function	1.17	3	6.11	0.491	2.62e-7	69

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000616	0.0000615
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000458	0.0000440
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May play an important role in maintaining normal growth homeostasis in epithelial cells. {ECO:0000269|PubMed:14583459}.
• Pathway: Autophagy - animal - Homo sapiens (human) (Consensus)

Recessive Scores

• pRec: 0.0739

Intolerance Scores

• loftool: 0.842
• rvis_EVS: 0.48
• rvis_percentile_EVS: 79.25

Haploinsufficiency Scores

• pHI: 0.0879
• hipred: N
• hipred_score: 0.123
• ghis: 0.394

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.0127

Mouse Genome Informatics

• Gene name: Prap1
• Phenotype: immune system phenotype; hematopoietic system phenotype

Gene ontology

• Biological process: regulation of transcription by RNA polymerase II
• Cellular component: extracellular region
• Molecular function: DNA-binding transcription factor activity, RNA polymerase II-specific;protein binding