PRND

prion like protein doppel

Basic information

Region (hg38): 20:4721909-4728460

Links

ENSG00000171864 ∙ NCBI:23627 ∙ OMIM:604263 ∙ HGNC:15748 ∙ Uniprot:Q9UKY0 ∙ 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 PRND gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PRND 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			9		1	10
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding				1		1
Total	0	0	9	1	1

Variants in PRND

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

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

Position	Type	Phenotype	Significance	ClinVar
20-4724550-C-T			Likely benign (Aug 01, 2023)
20-4724585-A-G		not specified	Uncertain significance (Jan 09, 2023)
20-4724634-G-A		not specified	Uncertain significance (Oct 10, 2023)
20-4724667-C-T		not specified	Uncertain significance (Apr 07, 2023)
20-4724669-C-G		not specified	Uncertain significance (Jan 09, 2025)
20-4724718-C-T			Benign (Jul 27, 2018)
20-4724808-C-T		not specified	Uncertain significance (Jan 30, 2024)
20-4724810-G-A		not specified	Uncertain significance (Nov 27, 2024)
20-4724861-T-C		not specified	Uncertain significance (Jan 24, 2025)
20-4724870-G-A		not specified	Likely benign (Jan 19, 2025)
20-4724945-C-G		not specified	Uncertain significance (Jan 26, 2023)
20-4724951-C-T		not specified	Uncertain significance (Jan 07, 2025)
20-4724969-T-A		not specified	Uncertain significance (Dec 05, 2022)
20-4724975-C-T		not specified	Uncertain significance (Mar 17, 2023)
20-4725066-G-T		not specified	Uncertain significance (Dec 28, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PRND	protein_coding	protein_coding	ENST00000305817	1	6551

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0125	0.669	125729	0	5	125734	0.0000199

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.106	105	102	1.03	0.00000633	1157
Missense in Polyphen		35	30.001	1.1666		347
Synonymous	-0.469	49	45.0	1.09	0.00000325	340
Loss of Function	0.522	3	4.15	0.723	1.84e-7	42

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000289	0.0000289
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000544	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.00000880	0.00000879
Middle Eastern	0.0000544	0.0000544
South Asian	0.0000653	0.0000653
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Required for normal acrosome reaction and for normal male fertility (By similarity). Can bind Cu(2+) (PubMed:15218028, PubMed:20411530). {ECO:0000250|UniProtKB:Q9QUG3, ECO:0000269|PubMed:15218028, ECO:0000269|PubMed:20411530}.
• Pathway: Post-translational modification: synthesis of GPI-anchored proteins;Post-translational protein modification;Metabolism of proteins (Consensus)

Recessive Scores

• pRec: 0.174

Intolerance Scores

• loftool: 0.237
• rvis_EVS: 0.31
• rvis_percentile_EVS: 72.23

Haploinsufficiency Scores

• pHI: 0.152
• hipred: N
• hipred_score: 0.146

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.0975

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Prnd
• Phenotype: reproductive system phenotype; cellular phenotype

Gene ontology

• Biological process: cellular copper ion homeostasis;acrosome reaction;protein homooligomerization
• Cellular component: extracellular region;plasma membrane;anchored component of external side of plasma membrane
• Molecular function: copper ion binding