PRRT3

proline rich transmembrane protein 3

Basic information

Region (hg38): 3:9939449-9952408

Links

ENSG00000163704 ∙ NCBI:285368 ∙ OMIM:619993 ∙ HGNC:26591 ∙ Uniprot:Q5FWE3 ∙ 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 PRRT3 gene.

• Inborn genetic diseases (43 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PRRT3 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			43			43
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	43	0	0

Variants in PRRT3

This is a list of pathogenic ClinVar variants found in the PRRT3 region.

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

Position	Type	Phenotype	Significance	ClinVar
3-9940633-A-G			Benign (Nov 12, 2018)
3-9940761-A-G			Benign (May 11, 2021)
3-9940761-A-AAGGGAGAGGGAG			Benign (May 11, 2021)
3-9940873-C-G		Atrioventricular septal defect, susceptibility to, 2	risk factor (Jun 01, 2005)
3-9940879-G-A		Inborn genetic diseases	Uncertain significance (Aug 12, 2022)
3-9940887-C-T		not specified • Atrioventricular septal defect, susceptibility to, 2 • CRELD1-related disorder	Benign/Likely benign (Feb 16, 2024)
3-9940912-C-T		Atrioventricular septal defect, susceptibility to, 2	Uncertain significance (Jul 22, 2017)
3-9940913-G-A		Atrioventricular septal defect, susceptibility to, 2	Uncertain significance (Aug 28, 2021)
3-9940950-C-T			Likely benign (Nov 01, 2023)
3-9940950-CG-C		Atrioventricular septal defect, susceptibility to, 2	Uncertain significance (Nov 06, 2021)
3-9940951-G-A		Atrioventricular septal defect, susceptibility to, 2 • Inborn genetic diseases	Uncertain significance (Mar 13, 2023)
3-9940954-G-A		Atrioventricular septal defect, susceptibility to, 2	Uncertain significance (Jan 14, 2022)
3-9940964-G-A		Atrioventricular septal defect, susceptibility to, 2 • CRELD1-related disorder • Jeffries-Lakhani neurodevelopmental syndrome	Uncertain significance (Aug 01, 2023)
3-9940976-G-T		Ventricular septal defect 1	Pathogenic (-)
3-9940989-T-C		Atrioventricular septal defect, susceptibility to, 2	Likely benign (Jun 25, 2021)
3-9941000-G-A		Atrioventricular septal defect, susceptibility to, 2	Uncertain significance (Oct 24, 2022)
3-9941002-A-G		Atrioventricular septal defect, susceptibility to, 2	Uncertain significance (Jun 27, 2022)
3-9941005-G-A		Atrioventricular septal defect, susceptibility to, 2	Benign (Nov 27, 2023)
3-9941024-C-T		Atrioventricular septal defect, susceptibility to, 2 • Inborn genetic diseases	Uncertain significance (Mar 28, 2023)
3-9941025-G-A		Atrioventricular septal defect, susceptibility to, 2	Likely benign (Sep 15, 2023)
3-9941046-G-A		Atrioventricular septal defect, susceptibility to, 2	Benign (Jul 05, 2022)
3-9941131-C-T		Atrioventricular septal defect, susceptibility to, 2	Uncertain significance (Dec 28, 2020)
3-9941132-G-A		Atrioventricular septal defect, susceptibility to, 2 • Inborn genetic diseases	Conflicting classifications of pathogenicity (Dec 06, 2022)
3-9941134-T-C		Atrioventricular septal defect, susceptibility to, 2	Uncertain significance (Nov 05, 2023)
3-9941139-A-G		Atrioventricular septal defect, susceptibility to, 2	Likely benign (Jan 15, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PRRT3	protein_coding	protein_coding	ENST00000412055	3	6853

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0000538	0.994	124737	0	17	124754	0.0000681

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.35	426	512	0.832	0.0000284	5977
Missense in Polyphen		147	184.59	0.79636		2317
Synonymous	0.811	224	240	0.933	0.0000143	2324
Loss of Function	2.43	11	23.8	0.462	0.00000129	262

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000199	0.000187
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000995	0.0000883
Middle Eastern	0.00	0.00
South Asian	0.0000984	0.0000980
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Recessive Scores

• pRec: 0.0891

Haploinsufficiency Scores

• pHI: 0.107
• hipred: N
• hipred_score: 0.458
• ghis: 0.501

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.351

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Prrt3

Gene ontology

• Cellular component: integral component of membrane