PTTG2

pituitary tumor-transforming 2

Basic information

Region (hg38): 4:37960397-37961128

Links

ENSG00000250254 ∙ NCBI:10744 ∙ OMIM:604231 ∙ HGNC:9691 ∙ Uniprot:Q9NZH5 ∙ 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 PTTG2 gene.

• Inborn genetic diseases (11 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PTTG2 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			10	1		11
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	10	1	0

Variants in PTTG2

This is a list of pathogenic ClinVar variants found in the PTTG2 region.

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

Position	Type	Phenotype	Significance	ClinVar
4-37960475-C-G		not specified	Uncertain significance (Jun 05, 2023)
4-37960483-C-T		not specified	Uncertain significance (Jun 18, 2021)
4-37960484-G-A		not specified	Uncertain significance (Mar 31, 2022)
4-37960592-C-T		not specified	Uncertain significance (May 17, 2023)
4-37960612-A-G		not specified	Uncertain significance (Dec 05, 2022)
4-37960628-G-A		not specified	Uncertain significance (Dec 02, 2022)
4-37960695-C-A		not specified	Uncertain significance (Mar 13, 2023)
4-37960706-A-G		not specified	Likely benign (Mar 24, 2023)
4-37960713-G-A		not specified	Uncertain significance (Jun 22, 2023)
4-37960717-G-A		not specified	Uncertain significance (Aug 02, 2021)
4-37960732-A-G		not specified	Uncertain significance (Oct 12, 2021)
4-37960834-C-T		not specified	Uncertain significance (Dec 11, 2023)
4-37960862-G-A		not specified	Uncertain significance (Oct 13, 2023)
4-37960940-T-G		not specified	Uncertain significance (May 05, 2023)
4-37960964-A-G		not specified	Uncertain significance (May 18, 2022)
4-37960967-T-C		not specified	Uncertain significance (Nov 21, 2023)
4-37960999-C-A		not specified	Uncertain significance (Feb 12, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PTTG2	protein_coding	protein_coding	ENST00000504686	1	691

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.422	113	101	1.12	0.00000540	1225
Missense in Polyphen		24	24.126	0.9948		351
Synonymous	-0.719	45	39.3	1.15	0.00000216	400
Loss of Function

LoF frequencies by population

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

dbNSFP

Source: dbNSFP

• Pathway: Cell cycle - Homo sapiens (human);Oocyte meiosis - Homo sapiens (human);HTLV-I infection - Homo sapiens (human);Cell Cycle (Consensus)

Recessive Scores

• pRec: 0.317

Intolerance Scores

• loftool: 0.799
• rvis_EVS: 0.35
• rvis_percentile_EVS: 74.18

Haploinsufficiency Scores

• hipred: N
• hipred_score: 0.112
• ghis: 0.406

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.114

Gene Damage Prediction

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

Gene ontology

• Biological process: homologous chromosome segregation;chromosome organization;negative regulation of mitotic sister chromatid separation
• Cellular component: nucleus;cytoplasm
• Molecular function: molecular_function;SH3 domain binding