TNP1

transition protein 1

Basic information

Region (hg38): 2:216859458-216860064

Links

ENSG00000118245 ∙ NCBI:7141 ∙ OMIM:190231 ∙ HGNC:11951 ∙ Uniprot:P09430 ∙ 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 TNP1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the TNP1 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			5			5
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	5	0	0

Variants in TNP1

This is a list of pathogenic ClinVar variants found in the TNP1 region.

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

Position	Type	Phenotype	Significance	ClinVar
2-216859675-G-C		not specified	Uncertain significance (May 29, 2024)
2-216859681-G-T		not specified	Uncertain significance (Oct 12, 2021)
2-216859687-T-C		not specified	Uncertain significance (Apr 06, 2024)
2-216859902-C-T		not specified	Uncertain significance (Sep 29, 2023)
2-216859938-A-G		not specified	Uncertain significance (Oct 18, 2021)
2-216860001-T-C		not specified	Uncertain significance (Oct 13, 2021)
2-216860021-C-T		not specified	Uncertain significance (Apr 28, 2023)
2-216860022-G-C		not specified	Uncertain significance (Jun 11, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
TNP1	protein_coding	protein_coding	ENST00000236979	2	607

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0376	0.654	125687	0	4	125691	0.0000159

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.0486	38	37.2	1.02	0.00000282	361
Missense in Polyphen		21	21.789	0.96381		187
Synonymous	-0.650	15	12.1	1.24	6.86e-7	99
Loss of Function	0.410	2	2.73	0.732	2.02e-7	29

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000152	0.000152
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.00000881	0.00000880
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Plays a key role in the replacement of histones to protamine in the elongating spermatids of mammals. In condensing spermatids, loaded onto the nucleosomes, where it promotes the recruitment and processing of protamines, which are responsible for histone eviction. {ECO:0000250|UniProtKB:P10856}.

Intolerance Scores

• loftool: 0.267
• rvis_EVS: -0.01
• rvis_percentile_EVS: 52.85

Haploinsufficiency Scores

• pHI: 0.707
• hipred: N
• hipred_score: 0.170
• ghis: 0.512

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.539

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Tnp1
• Phenotype: cellular phenotype; reproductive system phenotype

Gene ontology

• Biological process: single strand break repair;nucleosome disassembly;chromatin remodeling;chromatin silencing;multicellular organism development;spermatid development;spermatid nucleus differentiation;spermatid nucleus elongation;positive regulation of protein processing;sexual reproduction;flagellated sperm motility;fertilization, exchange of chromosomal proteins;spermatogenesis, exchange of chromosomal proteins;negative regulation of transcription, DNA-templated
• Cellular component: nucleosome;nuclear nucleosome;male germ cell nucleus;nucleus
• Molecular function: DNA binding;protein binding