SSU72

SSU72 homolog, RNA polymerase II CTD phosphatase, the group of Serine/threonine phosphatases

Basic information

Region (hg38): 1:1541672-1574863

Links

ENSG00000160075 ∙ NCBI:29101 ∙ OMIM:617680 ∙ HGNC:25016 ∙ Uniprot:Q9NP77 ∙ 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 SSU72 gene.

• Inborn genetic diseases (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SSU72 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			1			1
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	1	0	0

Variants in SSU72

This is a list of pathogenic ClinVar variants found in the SSU72 region.

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

Position	Type	Phenotype	Significance	ClinVar
1-1542157-G-A		not specified	Uncertain significance (Jun 21, 2023)
1-1564800-T-C		not specified	Uncertain significance (Feb 28, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SSU72	protein_coding	protein_coding	ENST00000291386	5	33197

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.779	0.220	125744	0	3	125747	0.0000119

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.56	36	112	0.320	0.00000609	1286
Missense in Polyphen		6	29.29	0.20485		415
Synonymous	-0.450	52	48.0	1.08	0.00000308	344
Loss of Function	2.53	1	9.34	0.107	4.80e-7	109

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000289	0.0000289
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000177	0.0000176
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Protein phosphatase that catalyzes the dephosphorylation of the C-terminal domain of RNA polymerase II. Plays a role in RNA processing and termination. Plays a role in pre-mRNA polyadenylation via its interaction with SYMPK. {ECO:0000269|PubMed:15659578, ECO:0000269|PubMed:20861839, ECO:0000269|PubMed:23070812}.
• Pathway: mRNA surveillance pathway - Homo sapiens (human) (Consensus)

Recessive Scores

• pRec: 0.118

Intolerance Scores

• loftool: 0.508
• rvis_EVS: -0.14
• rvis_percentile_EVS: 42.88

Haploinsufficiency Scores

• pHI: 0.145
• hipred: Y
• hipred_score: 0.715
• ghis: 0.572

Essentials

• essential_gene_CRISPR: E
• essential_gene_CRISPR2: E
• essential_gene_gene_trap: E
• gene_indispensability_pred: E
• gene_indispensability_score: 0.964

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Low	Low	Low
Primary Immunodeficiency	Low	Low	Low
Cancer	Low	Low	Low

Mouse Genome Informatics

• Gene name: Ssu72

Gene ontology

• Biological process: termination of RNA polymerase II transcription;mRNA polyadenylation;dephosphorylation of RNA polymerase II C-terminal domain
• Cellular component: nucleoplasm;cytosol;mRNA cleavage and polyadenylation specificity factor complex
• Molecular function: protein binding;RNA polymerase II CTD heptapeptide repeat phosphatase activity