TPRG1L

tumor protein p63 regulated 1 like

Basic information

Region (hg38): 1:3625014-3630127

Previous symbols: [ "FAM79A" ]

Links

ENSG00000158109 ∙ NCBI:127262 ∙ OMIM:611460 ∙ HGNC:27007 ∙ Uniprot:Q5T0D9 ∙ 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 TPRG1L gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the TPRG1L 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			15	2		17
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	15	2	0

Variants in TPRG1L

This is a list of pathogenic ClinVar variants found in the TPRG1L region.

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

Position	Type	Phenotype	Significance	ClinVar
1-3625088-G-T		not specified	Uncertain significance (Sep 09, 2021)
1-3625091-T-G		not specified	Uncertain significance (Jan 23, 2024)
1-3625157-G-T		not specified	Uncertain significance (Aug 12, 2021)
1-3625184-G-A		not specified	Likely benign (Sep 07, 2022)
1-3625194-C-T		not specified	Uncertain significance (May 12, 2024)
1-3625199-C-T		not specified	Uncertain significance (Jun 03, 2022)
1-3625254-A-G		not specified	Uncertain significance (Nov 18, 2022)
1-3625757-C-T		not specified	Uncertain significance (Mar 01, 2024)
1-3625760-A-T		not specified	Uncertain significance (Oct 06, 2022)
1-3625832-A-G		not specified	Likely benign (Dec 14, 2022)
1-3625850-C-T		not specified	Uncertain significance (Jul 09, 2021)
1-3627539-A-T		not specified	Uncertain significance (Sep 06, 2022)
1-3627564-T-C		not specified	Uncertain significance (Mar 23, 2022)
1-3627579-A-G		not specified	Uncertain significance (Feb 15, 2023)
1-3627583-A-C		not specified	Uncertain significance (May 20, 2024)
1-3627585-G-A		not specified	Uncertain significance (Oct 03, 2022)
1-3628505-C-T		not specified	Uncertain significance (May 18, 2023)
1-3628506-G-A		not specified	Uncertain significance (Jun 29, 2023)
1-3628538-A-T		not specified	Uncertain significance (Dec 13, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
TPRG1L	protein_coding	protein_coding	ENST00000378344	5	5126

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
8.47e-7	0.314	125365	1	381	125747	0.00152

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.784	98	122	0.801	0.00000670	1735
Missense in Polyphen		40	44.343	0.90206		538
Synonymous	-1.37	62	49.7	1.25	0.00000295	563
Loss of Function	0.372	10	11.4	0.881	5.70e-7	131

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00102	0.00102
Ashkenazi Jewish	0.000701	0.000695
East Asian	0.0000544	0.0000544
Finnish	0.000693	0.000693
European (Non-Finnish)	0.00287	0.00286
Middle Eastern	0.0000544	0.0000544
South Asian	0.000164	0.000163
Other	0.000815	0.000815

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Presynaptic protein involved in the synaptic transmission tuning. Regulates synaptic release probability by decreasing the calcium sensitivity of release. {ECO:0000250|UniProtKB:A8WCF8}.

Recessive Scores

• pRec: 0.109

Intolerance Scores

• loftool: 0.447
• rvis_EVS: -0.12
• rvis_percentile_EVS: 44.89

Haploinsufficiency Scores

• pHI: 0.157
• hipred: N
• hipred_score: 0.466
• ghis: 0.561

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.601

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Tprgl

Gene ontology

• Biological process: biological_process;regulation of synaptic transmission, glutamatergic
• Cellular component: cytoplasm;synaptic vesicle;cell junction;synaptic vesicle membrane;calyx of Held;extracellular exosome
• Molecular function: molecular_function;identical protein binding