SSU72

protein-coding

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

Gene summary

Enables RNA polymerase II CTD heptapeptide repeat phosphatase activity. Involved in co-transcriptional mRNA 3'-end processing, cleavage and polyadenylation pathway. Predicted to be located in cytoplasm and nucleus. Predicted to be part of mRNA cleavage and polyadenylation specificity factor complex. [provided by Alliance of Genome Resources, Jun 2026]

MANE transcript

NM_014188.3

Inheritance

—

ClinVar variants

U:13

Top phenotype

Autosomal recessive osteopetrosis 4

gnomAD constraint

pLI —, LoF o/e 0.11

Max pathogenic AF

—

Genomic locus

chr1:1,541,673-1,574,863

External References & Databases

Ensembl (ENSG00000160075)

Transcript & Mutation Effects

hg38 • Region Span ~33.2 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to SSU72 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 11

Autosomal recessive osteopetrosis 4Total: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_014188.3. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous						0
missense			13 clinvar			13
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	13	0	0	13

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 19 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_014188.3	RefSeq	NP_054907.1	5	MANE Select
ENST00000291386.4	Ensembl	ENSP00000291386.3	5	MANE Select
ENST00000359060.5	Ensembl	ENSP00000351955.3	2	Standard
ENST00000359060.6	Ensembl	ENSP00000351955.3	2	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

mRNA surveillance pathway - Homo sapiens (human)

Biological Process

termination of RNA polymerase II transcription
mRNA polyadenylation
dephosphorylation of RNA polymerase II C-terminal domain

Molecular Function

protein binding
RNA polymerase II CTD heptapeptide repeat phosphatase activity

Cellular Component

nucleoplasm
cytosol
mRNA cleavage and polyadenylation specificity factor complex

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000291386
Coding exons: 5
Length: 33197
Individuals with no LoFs: 125744
Homozygous LoFs: 0
Heterozygous LoFs: 3
Defined: 125747
p: 0.0000119

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	2.56	36	112	0.320	0.00000609	1286
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0	0.0	absent
Latino/Admixed American	0.000029	0.000029	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0	0.0	absent
Finnish	0	0.0	absent
European (Non-Finnish)	0.000018	0.000018	rare
South Asian	0	0.0	absent
Other	0	0.0	absent

dbNSFP Gene Annotations

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}.;

Recessive Scores

pRec: 0.118

Intolerance Scores

LoFtool: 0.508
RVIS EVS: -0.14
RVIS percentile EVS: 42.88

Essentials

Essential (CRISPR): E
Essential (CRISPR2): E
Essential (gene trap): E
Indispensability pred.: E
Indispensability score: 0.964

Gene Damage Prediction

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