PRND

protein-coding

prion like protein doppel

Gene summary

This gene is found on chromosome 20, approximately 20 kbp downstream of the gene encoding cellular prion protein, to which it is biochemically and structurally similar. The protein encoded by this gene is a membrane glycosylphosphatidylinositol-anchored glycoprotein that is found predominantly in testis. Mutations in this gene may lead to neurological disorders. [provided by RefSeq, Jul 2008]

MANE transcript

NM_012409.4

Inheritance

—

ClinVar variants

U:23B:3

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.72

Max pathogenic AF

—

Genomic locus

chr20:4,721,909-4,728,460

External References & Databases

Ensembl (ENSG00000171864)

Transcript & Mutation Effects

hg38 • Region Span ~6.6 kb

Loading mutation effect viewer...

GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to PRND variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 23

not providedTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_012409.4. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous			1 clinvar			1
missense			22 clinvar	2 clinvar	1 clinvar	25
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	23	2	1	26

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 2 of 2 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_012409.4	RefSeq	NP_036541.2	1	MANE Select
ENST00000305817.3	Ensembl	ENSP00000306900.2	1	MANE Select

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

Post-translational modification: synthesis of GPI-anchored proteins
Post-translational protein modification
Metabolism of proteins

Biological Process

cellular copper ion homeostasis
acrosome reaction
protein homooligomerization

Molecular Function

copper ion binding

Cellular Component

extracellular region
plasma membrane
anchored component of external side of plasma membrane

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000305817
Coding exons: 1
Length: 6551
Individuals with no LoFs: 125729
Homozygous LoFs: 0
Heterozygous LoFs: 5
Defined: 125734
p: 0.0000199

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	-0.106	105	102	1.03	0.00000633	1157
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0	0.0	absent
Latino/Admixed American	0.000029	0.000029	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0.000054	0.000054	rare
Finnish	0	0.0	absent
European (Non-Finnish)	0.0000088	0.0000088	rare
South Asian	0.000065	0.000065	rare
Other	0	0.0	absent

dbNSFP Gene Annotations

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}.;

Recessive Scores

pRec: 0.174

Intolerance Scores

LoFtool: 0.237
RVIS EVS: 0.31
RVIS percentile EVS: 72.23

Essentials

Essential (CRISPR): N
Essential (CRISPR2): S
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.0975

Gene Damage Prediction

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