PRTG

protein-coding

protogenin, the group of Fibronectin type III domain containing|I-set domain containing

Gene summary

This gene encodes a member of the immunoglobulin superfamily. The encoded transmembrane protein has been associated with the development of various tissues, especially neurogenesis. It has been suggested that this gene may be associated with attention deficit hyperactivity disorder (ADHD). [provided by RefSeq, Nov 2014]

MANE transcript

NM_173814.6

Inheritance

—

ClinVar variants

U:146B:9

Top phenotype

See cases

gnomAD constraint

pLI —, LoF o/e 0.39

Max pathogenic AF

—

Genomic locus

chr15:55,611,544-55,743,152

External References & Databases

Ensembl (ENSG00000166450)

Transcript & Mutation Effects

hg38 • Region Span ~131.6 kb

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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 PRTG variants in ClinVar

3 Conditions Cataloged

not specifiedTotal: 140

not providedTotal: 9

See casesTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_173814.6. 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			2 clinvar	1 clinvar	1 clinvar	4
missense			140 clinvar	6 clinvar	1 clinvar	147
nonsense			1 clinvar			1
start loss						0
frameshift			1 clinvar			1
splice donor/acceptor (+/-2bp)			2 clinvar			2
Total	0	0	146	7	2	155

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 13 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_173814.6	RefSeq	NP_776175.2	20	MANE Select
ENST00000389286.9	Ensembl	ENSP00000373937.4	20	MANE Select
ENST00000558349.1	Ensembl	ENSP00000452760.1	1	Standard
ENST00000561292.1	Ensembl	ENSP00000453335.1	3	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

Neural Crest Differentiation

Biological Process

negative regulation of neurogenesis
protein homooligomerization

Molecular Function

signaling receptor activity

Cellular Component

extracellular space
plasma membrane
integral component of membrane

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000389286
Coding exons: 20
Length: 131545
Individuals with no LoFs: 124744
Homozygous LoFs: 0
Heterozygous LoFs: 52
Defined: 124796
p: 0.000208

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.393	601	629	0.956	0.0000330	7402
Missense (PolyPhen)		209	261.15	0.8003		3050
Synonymous	-1.29	249	224	1.11	0.0000115	2342
Loss of Function	4.20	22	55.9	0.393	0.00000298	669

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00019	0.00019	rare
Latino/Admixed American	0.00020	0.00020	rare
Ashkenazi Jewish	0.00010	0.000099	rare
East Asian	0.00022	0.00022	rare
Finnish	0.000047	0.000046	rare
European (Non-Finnish)	0.00023	0.00023	rare
South Asian	0.00026	0.00026	rare
Other	0.00033	0.00033	rare

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: May play a role in anteroposterior axis elongation. {ECO:0000250|UniProtKB:Q2EY15}.;

Recessive Scores

pRec: 0.103

Intolerance Scores

LoFtool: 0.675
RVIS EVS: -0.06
RVIS percentile EVS: 48.91

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.313

Gene Damage Prediction

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