PRRT1

proline rich transmembrane protein 1, the group of interferon induced transmembrane protein domain containing

Basic information

Region (hg38): 6:32148358-32153083

Previous symbols: [ "C6orf31" ]

Links

ENSG00000204314 ∙ NCBI:80863 ∙ OMIM:618297 ∙ HGNC:13943 ∙ Uniprot:Q99946 ∙ 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 PRRT1 gene.

• Inborn genetic diseases (7 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PRRT1 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			7			7
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	7	0	0

Variants in PRRT1

This is a list of pathogenic ClinVar variants found in the PRRT1 region.

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

Position	Type	Phenotype	Significance	ClinVar
6-32149554-T-C		not specified	Uncertain significance (May 27, 2022)
6-32150442-C-T		not specified	Uncertain significance (Aug 14, 2023)
6-32150519-G-A		not specified	Uncertain significance (Aug 23, 2021)
6-32150606-A-G		not specified	Uncertain significance (Oct 02, 2023)
6-32150757-G-A		not specified	Uncertain significance (Mar 20, 2023)
6-32150822-T-G		not specified	Uncertain significance (Nov 02, 2023)
6-32150864-T-C		not specified	Uncertain significance (Dec 06, 2021)
6-32150888-G-A		not specified	Uncertain significance (Mar 24, 2023)
6-32151815-T-C		not specified	Uncertain significance (Jan 10, 2022)
6-32151818-C-G		not specified	Uncertain significance (Jan 23, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PRRT1	protein_coding	protein_coding	ENST00000211413	4	6015

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.298	0.684	122136	0	1	122137	0.00000409

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	3.03	59	170	0.347	0.0000109	1868
Missense in Polyphen		9	43.887	0.20507		409
Synonymous	3.47	42	81.9	0.513	0.00000603	721
Loss of Function	2.00	2	8.15	0.245	3.47e-7	101

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000291	0.0000291
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

Recessive Scores

• pRec: 0.0322

Haploinsufficiency Scores

• pHI: 0.00984
• hipred: N
• hipred_score: 0.450
• ghis: 0.485

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.000401

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Prrt1
• Phenotype: behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan)

Gene ontology

• Cellular component: membrane;cell junction;glutamatergic synapse;integral component of postsynaptic membrane