TNP2

transition protein 2

Basic information

Region (hg38): 16:11267748-11269533

Links

ENSG00000178279 ∙ NCBI:7142 ∙ OMIM:190232 ∙ HGNC:11952 ∙ Uniprot:Q05952 ∙ 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 TNP2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the TNP2 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				1	1	2
missense			14			14
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	14	1	1

Variants in TNP2

This is a list of pathogenic ClinVar variants found in the TNP2 region.

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

Position	Type	Phenotype	Significance	ClinVar
16-11268000-T-C		not specified	Uncertain significance (Oct 12, 2021)
16-11268874-G-A		not specified	Uncertain significance (Aug 17, 2022)
16-11268884-T-C		not specified	Uncertain significance (Sep 14, 2022)
16-11268884-T-G		not specified	Uncertain significance (Mar 24, 2023)
16-11268922-T-C		not specified	Uncertain significance (Aug 02, 2021)
16-11268937-A-G		not specified	Uncertain significance (Jun 09, 2022)
16-11268948-G-A			Likely benign (Dec 01, 2022)
16-11268961-C-G		not specified	Uncertain significance (Apr 07, 2023)
16-11268961-C-T		not specified	Uncertain significance (May 31, 2023)
16-11268976-G-A		not specified	Uncertain significance (May 25, 2022)
16-11269054-C-G		not specified	Uncertain significance (Aug 10, 2021)
16-11269130-G-A		not specified	Uncertain significance (Jul 13, 2022)
16-11269134-G-T			Benign (May 21, 2018)
16-11269193-G-A		not specified	Uncertain significance (Nov 07, 2023)
16-11269241-G-C		not specified	Uncertain significance (Jul 20, 2022)
16-11269259-C-T		not specified	Uncertain significance (Mar 02, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
TNP2	protein_coding	protein_coding	ENST00000312693	2	1786

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00915	0.602	123443	0	1	123444	0.00000405

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.544	99	84.9	1.17	0.00000527	919
Missense in Polyphen		9	6.6235	1.3588		67
Synonymous	-2.07	43	28.9	1.49	0.00000152	243
Loss of Function	0.286	3	3.58	0.837	1.52e-7	44

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	0.0000334	0.0000334
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:P11378}.

Recessive Scores

• pRec: 0.106

Intolerance Scores

• rvis_EVS: 0.55
• rvis_percentile_EVS: 81.38

Haploinsufficiency Scores

• pHI: 0.590
• hipred: N
• hipred_score: 0.123

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.191

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Tnp2
• Phenotype: cellular phenotype; reproductive system phenotype; normal phenotype

Gene ontology

• Biological process: multicellular organism development;spermatogenesis;acrosome reaction;penetration of zona pellucida;positive regulation of protein processing;spermatogenesis, exchange of chromosomal proteins
• Cellular component: nuclear nucleosome
• Molecular function: DNA binding;zinc ion binding