CTDSPL2

protein-coding

CTD small phosphatase like 2, the group of CTD family phosphatases

Gene summary

Enables RNA polymerase II CTD heptapeptide repeat phosphatase activity. Involved in positive regulation of gluconeogenesis. Located in nucleus. [provided by Alliance of Genome Resources, Jun 2026]

MANE transcript

NM_016396.3

Inheritance

—

ClinVar variants

U:54B:2

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.04

Max pathogenic AF

—

Genomic locus

chr15:44,427,622-44,529,038

External References & Databases

Ensembl (ENSG00000137770)

Transcript & Mutation Effects

hg38 • Region Span ~101.4 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 CTDSPL2 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 46

not providedTotal: 5

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_016396.3. 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			1 clinvar		1 clinvar	2
missense			47 clinvar		1 clinvar	48
nonsense			1 clinvar			1
start loss						0
frameshift			2 clinvar			2
splice donor/acceptor (+/-2bp)			3 clinvar			3
Total	0	0	54	0	2	56

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 47 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_016396.3	RefSeq	NP_057480.2	12	MANE Select
ENST00000260327.9	Ensembl	ENSP00000260327.4	12	MANE Select
ENST00000558373.5	Ensembl	ENSP00000453051.1	11	Standard
ENST00000558373.6	Ensembl	ENSP00000453051.1	11	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

protein dephosphorylation
negative regulation of BMP signaling pathway
positive regulation of protein export from nucleus

Molecular Function

phosphoprotein phosphatase activity

Cellular Component

nucleoplasm

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000260327
Coding exons: 12
Length: 101805
Individuals with no LoFs: 125096
Homozygous LoFs: 0
Heterozygous LoFs: 1
Defined: 125097
p: 0.00000400

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	2.20	149	246	0.605	0.0000129	3024
Missense (PolyPhen)		12	70.447	0.17034		905
Synonymous	0.816	76	85.6	0.888	0.00000440	882
Loss of Function	4.67	1	27.3	0.0366	0.00000148	340

Population LoF Frequency

Population	CAF	p-value	Status
African	0.000062	0.000062	rare
Latino/Admixed American	0	0.0	absent
Ashkenazi Jewish	0	0.0	absent
East Asian	0	0.0	absent
Finnish	0	0.0	absent
European (Non-Finnish)	0	0.0	absent
South Asian	0	0.0	absent
Other	0	0.0	absent

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: Probable phosphatase. {ECO:0000250}.;

Recessive Scores

pRec: 0.114

Intolerance Scores

LoFtool: 0.0922
RVIS EVS: -0.03
RVIS percentile EVS: 51.66

Essentials

Essential (CRISPR): E
Essential (CRISPR2): N
Essential (gene trap): E
Indispensability pred.: E
Indispensability score: 0.519

Gene Damage Prediction

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