PRRT4

proline rich transmembrane protein 4

Basic information

Region (hg38): 7:128350325-128361690

Links

ENSG00000224940 ∙ NCBI:401399 ∙ ∙ HGNC:37280 ∙ Uniprot:C9JH25 ∙ 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 PRRT4 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PRRT4 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				1		1
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	0	1	0

Variants in PRRT4

This is a list of pathogenic ClinVar variants found in the PRRT4 region.

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

Position	Type	Phenotype	Significance	ClinVar
7-128350882-C-T		not specified	Likely benign (Aug 29, 2024)
7-128350895-G-C		not specified	Uncertain significance (Feb 02, 2024)
7-128350899-T-G		not specified	Uncertain significance (Sep 17, 2021)
7-128350923-T-C		not specified	Uncertain significance (Nov 14, 2023)
7-128350974-T-A		not specified	Uncertain significance (Jan 22, 2025)
7-128351016-G-A		not specified	Uncertain significance (Nov 07, 2024)
7-128351026-G-C		not specified	Uncertain significance (Jul 25, 2024)
7-128351050-G-A		not specified	Uncertain significance (Sep 26, 2024)
7-128351079-G-T		not specified	Uncertain significance (Mar 15, 2024)
7-128351094-C-T		not specified	Uncertain significance (Dec 20, 2023)
7-128351110-T-G		not specified	Uncertain significance (Jul 05, 2023)
7-128351143-A-G		not specified	Uncertain significance (Nov 28, 2023)
7-128351146-C-T		not specified	Uncertain significance (Dec 12, 2023)
7-128351184-G-A		not specified	Uncertain significance (Oct 21, 2024)
7-128351199-G-A		not specified	Uncertain significance (Jun 29, 2023)
7-128351248-C-G		not specified	Uncertain significance (Feb 06, 2024)
7-128351250-G-A		not specified	Uncertain significance (Jun 04, 2024)
7-128351276-T-C		not specified	Likely benign (Aug 28, 2024)
7-128351293-C-A		not specified	Uncertain significance (Jun 22, 2021)
7-128351293-C-T		not specified	Uncertain significance (Feb 26, 2025)
7-128351334-A-G		not specified	Uncertain significance (Jan 04, 2022)
7-128351364-C-T		not specified	Uncertain significance (Sep 07, 2022)
7-128351383-G-C		not specified	Uncertain significance (Sep 30, 2024)
7-128351482-C-T		not specified	Uncertain significance (Nov 09, 2023)
7-128351509-G-T		not specified	Uncertain significance (Jan 30, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PRRT4	protein_coding	protein_coding	ENST00000446477	4	11361

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.000596	0.978	0	0	0	0	0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.67	280	371	0.755	0.0000218	5400
Missense in Polyphen		57	101.46	0.56178		1561
Synonymous	2.55	148	193	0.767	0.0000127	2202
Loss of Function	2.03	8	17.0	0.470	7.92e-7	224

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.00	0.00
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.114

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Prrt4

Gene ontology

• Cellular component: integral component of membrane