PRTG

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

Basic information

Region (hg38): 15:55611544-55743152

Links

ENSG00000166450 ∙ NCBI:283659 ∙ OMIM:613261 ∙ HGNC:26373 ∙ Uniprot:Q2VWP7 ∙ 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 PRTG gene.

• not_specified (128 variants)
• not_provided (9 variants)
• See_cases (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PRTG gene is commonly pathogenic or not. These statistics are base on transcript: NM_000173814.6. Only rare variants are included in the table.

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.

Effect	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous				1	1	2
missense			126	5	1	132
nonsense						0
start loss						0
frameshift			1			1
splice donor/acceptor (+/-2bp)						0
Total	0	0	127	6	2

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PRTG	protein_coding	protein_coding	ENST00000389286	20	131545

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.20e-7	1.00	124744	0	52	124796	0.000208

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.393	601	629	0.956	0.0000330	7402
Missense in 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

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000397	0.000397
Ashkenazi Jewish	0.000105	0.0000993
East Asian	0.000224	0.000223
Finnish	0.0000466	0.0000464
European (Non-Finnish)	0.000232	0.000230
Middle Eastern	0.000224	0.000223
South Asian	0.000262	0.000261
Other	0.000330	0.000330

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May play a role in anteroposterior axis elongation. {ECO:0000250|UniProtKB:Q2EY15}.
• Pathway: Neural Crest Differentiation (Consensus)

Recessive Scores

• pRec: 0.103

Intolerance Scores

• loftool: 0.675
• rvis_EVS: -0.06
• rvis_percentile_EVS: 48.91

Haploinsufficiency Scores

• pHI: 0.309
• hipred: Y
• hipred_score: 0.540
• ghis: 0.522

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.313

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Prtg

Gene ontology

• Biological process: negative regulation of neurogenesis;protein homooligomerization
• Cellular component: extracellular space;plasma membrane;integral component of membrane
• Molecular function: signaling receptor activity