TPRG1

tumor protein p63 regulated 1

Basic information

Region (hg38): 3:188947214-189325304

Previous symbols: [ "FAM79B" ]

Links

ENSG00000188001 ∙ NCBI:285386 ∙ ∙ HGNC:24759 ∙ Uniprot:Q6ZUI0 ∙ 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 TPRG1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the TPRG1 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			22			22
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	22	0	0

Variants in TPRG1

This is a list of pathogenic ClinVar variants found in the TPRG1 region.

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

Position	Type	Phenotype	Significance	ClinVar
3-189207445-G-A		not specified	Uncertain significance (Sep 20, 2023)
3-189207473-C-T		not specified	Uncertain significance (Jun 10, 2022)
3-189207527-C-T		not specified	Uncertain significance (Jan 23, 2024)
3-189207566-A-C		not specified	Uncertain significance (Jul 06, 2021)
3-189207570-C-G		not specified	Uncertain significance (Mar 25, 2024)
3-189207574-C-T		not specified	Uncertain significance (Mar 24, 2023)
3-189207575-G-A		not specified	Uncertain significance (Aug 17, 2021)
3-189215334-G-A		not specified	Likely benign (May 06, 2024)
3-189215340-G-C		not specified	Uncertain significance (May 11, 2022)
3-189215359-T-C		not specified	Uncertain significance (Oct 10, 2023)
3-189215364-G-A		not specified	Uncertain significance (May 22, 2023)
3-189215373-C-T		not specified	Uncertain significance (Feb 08, 2023)
3-189238795-T-C		not specified	Uncertain significance (Sep 16, 2021)
3-189238854-G-A		not specified	Uncertain significance (Dec 21, 2022)
3-189238864-G-C		not specified	Uncertain significance (Aug 08, 2023)
3-189310390-C-A		not specified	Uncertain significance (Jun 29, 2023)
3-189310390-C-G		not specified	Uncertain significance (Jun 12, 2023)
3-189310400-G-A		not specified	Uncertain significance (Jun 21, 2023)
3-189310431-G-T		not specified	Uncertain significance (Aug 17, 2022)
3-189310501-A-G		not specified	Uncertain significance (Sep 14, 2021)
3-189320659-A-C		not specified	Uncertain significance (Jun 06, 2023)
3-189320773-C-T		not specified	Uncertain significance (Apr 12, 2022)
3-189320797-G-T		not specified	Uncertain significance (Jun 24, 2022)
3-189320801-G-A		not specified	Uncertain significance (Jun 24, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
TPRG1	protein_coding	protein_coding	ENST00000345063	5	378091

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.94e-10	0.0356	125668	0	77	125745	0.000306

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.482	169	152	1.11	0.00000831	1781
Missense in Polyphen		49	47.16	1.039		565
Synonymous	-0.298	57	54.2	1.05	0.00000294	531
Loss of Function	-0.421	14	12.4	1.13	5.23e-7	164

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000728	0.000728
Ashkenazi Jewish	0.0000994	0.0000992
East Asian	0.000222	0.000217
Finnish	0.0000463	0.0000462
European (Non-Finnish)	0.000391	0.000387
Middle Eastern	0.000222	0.000217
South Asian	0.000238	0.000229
Other	0.000326	0.000326

dbNSFP

Source: dbNSFP

Recessive Scores

• pRec: 0.107

Intolerance Scores

• loftool: 0.356
• rvis_EVS: 0.06
• rvis_percentile_EVS: 58.53

Haploinsufficiency Scores

• pHI: 0.183
• hipred: N
• hipred_score: 0.282
• ghis: 0.516

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.317

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Tprg

Gene ontology

• Cellular component: cytoplasm