TRNP1

TMF1 regulated nuclear protein 1

Basic information

Region (hg38): 1:26993691-27000886

Previous symbols: [ "C1orf225" ]

Links

ENSG00000253368 ∙ NCBI:388610 ∙ OMIM:616824 ∙ HGNC:34348 ∙ Uniprot:Q6NT89 ∙ 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 TRNP1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the TRNP1 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	1		16
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	1	0

Variants in TRNP1

This is a list of pathogenic ClinVar variants found in the TRNP1 region.

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

Position	Type	Phenotype	Significance	ClinVar
1-26993823-G-A		not specified	Uncertain significance (Jan 20, 2023)
1-26993856-C-T		not specified	Uncertain significance (Sep 16, 2021)
1-26993868-G-T		not specified	Uncertain significance (Aug 02, 2021)
1-26993878-C-G		not specified	Uncertain significance (Nov 13, 2023)
1-26993916-C-G		not specified	Uncertain significance (Jun 18, 2024)
1-26993932-G-C		not specified	Likely benign (May 03, 2023)
1-26994039-G-A		not specified	Uncertain significance (Aug 01, 2022)
1-26994042-C-T		not specified	Uncertain significance (Feb 06, 2024)
1-26994048-G-T		not specified	Uncertain significance (Jan 26, 2022)
1-26994073-C-T		not specified	Uncertain significance (May 13, 2024)
1-26994075-G-C		not specified	Uncertain significance (Jan 07, 2022)
1-26994180-C-G		not specified	Uncertain significance (Jan 17, 2024)
1-26994198-G-A		not specified	Uncertain significance (Mar 30, 2024)
1-26994303-C-T		not specified	Uncertain significance (Feb 07, 2023)
1-26994315-C-T		not specified	Uncertain significance (May 29, 2024)
1-26994384-G-A		not specified	Uncertain significance (Nov 13, 2023)
1-26994384-G-C		not specified	Uncertain significance (Sep 22, 2023)
1-26994411-G-C		not specified	Uncertain significance (Sep 25, 2023)
1-26994429-C-A		not specified	Uncertain significance (Mar 02, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
TRNP1	protein_coding	protein_coding	ENST00000522111	1	7192

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.379	0.488	0	0	0	0	0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.640	13	21.3	0.610	0.00000112	1334
Missense in Polyphen		0	0.35876	0		71
Synonymous	0.568	8	10.3	0.775	5.53e-7	569
Loss of Function	0.867	0	0.876	0.00	3.87e-8	45

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

• Function: FUNCTION: DNA-binding factor that regulates the expression of a subset of genes and plays a key role in tangential, radial, and lateral expansion of the brain neocortex. Regulates neural stem cells proliferation and the production of intermediate neural progenitors and basal radial glial cells affecting the process of cerebral cortex gyrification. May control the proliferation rate of cells by regulating their progression through key cell-cycle transition points (By similarity). {ECO:0000250}.

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.283

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Trnp1

Gene ontology

• Biological process: cell cycle;cerebellar cortex morphogenesis;regulation of cell population proliferation;regulation of cell cycle;neural precursor cell proliferation
• Cellular component: nucleus;nuclear euchromatin
• Molecular function: DNA binding