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.

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.

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				1	1	2
missense			78	2	1	81
nonsense						0
start loss						0
frameshift			1			1
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region				1		1
non coding						0
Total	0	0	79	3	2

Variants in PRTG

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

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

Position	Type	Phenotype	Significance	ClinVar
15-55620020-TG-T			Uncertain significance (Jun 20, 2022)
15-55620193-G-A			Uncertain significance (Jun 20, 2022)
15-55620701-A-C		not specified	Conflicting classifications of pathogenicity (Feb 01, 2025)
15-55620713-T-C		not specified	Uncertain significance (Aug 14, 2024)
15-55620731-T-C		not specified	Uncertain significance (Jan 30, 2024)
15-55620752-T-C		not specified	Uncertain significance (May 12, 2024)
15-55624352-A-G		not specified	Uncertain significance (Nov 26, 2024)
15-55624371-T-C		not specified	Uncertain significance (Jul 12, 2022)
15-55624374-T-C		not specified	Uncertain significance (Apr 15, 2024)
15-55624386-A-T		not specified	Uncertain significance (Dec 22, 2023)
15-55624477-A-T		not specified	Uncertain significance (Jun 21, 2021)
15-55624478-T-C		not specified	Uncertain significance (Dec 25, 2024)
15-55627020-C-T		not specified	Uncertain significance (Sep 08, 2024)
15-55627024-A-C		not specified	Uncertain significance (Nov 06, 2024)
15-55627042-A-C		not specified	Uncertain significance (Oct 12, 2021)
15-55627107-A-T		not specified	Uncertain significance (Jul 13, 2022)
15-55628976-G-T		not specified	Uncertain significance (Jul 25, 2024)
15-55629004-C-G		not specified	Uncertain significance (Aug 02, 2021)
15-55637175-C-T		not specified	Uncertain significance (Sep 04, 2024)
15-55637176-G-A		not specified	Uncertain significance (Jan 26, 2022)
15-55637323-C-G		not specified	Uncertain significance (Sep 29, 2022)
15-55638573-C-T		not specified	Uncertain significance (Jan 24, 2023)
15-55638614-C-T		not specified	Uncertain significance (Nov 13, 2024)
15-55638618-C-T		not specified	Uncertain significance (Oct 04, 2022)
15-55639765-G-A		not specified	Uncertain significance (Jan 23, 2024)

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