CTTNBP2NL

protein-coding

CTTNBP2 N-terminal like, the group of STRIPAK complex

Gene summary

Enables protein phosphatase 2A binding activity. Acts upstream of or within negative regulation of transmembrane transport; negative regulation of transporter activity; and protein dephosphorylation. Located in actin cytoskeleton. Part of FAR/SIN/STRIPAK complex. [provided by Alliance of Genome Resources, Jul 2025]

MANE transcript

NM_018704.3

Inheritance

—

ClinVar variants

U:84B:5

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.38

Max pathogenic AF

—

Genomic locus

chr1:112,396,214-112,463,456

External References & Databases

Ensembl (ENSG00000143079)

Transcript & Mutation Effects

hg38 • Region Span ~67.2 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 CTTNBP2NL variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 83

not providedTotal: 2

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_018704.3. 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
missense			83 clinvar	3 clinvar	2 clinvar	88
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	84	3	2	89

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 29 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_018704.3	RefSeq	NP_061174.1	4	MANE Select
ENST00000271277.11	Ensembl	ENSP00000271277.6	4	MANE Select
ENST00000441739.1	Ensembl	ENSP00000390976.1	4	Standard
ENST00000862867.1	Ensembl	ENSP00000532926.1	4	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

protein dephosphorylation
negative regulation of transporter activity
negative regulation of transmembrane transport

Molecular Function

protein binding
protein phosphatase 2A binding

Cellular Component

cytoplasm
actin cytoskeleton

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000271277
Coding exons: 4
Length: 67276
Individuals with no LoFs: 125727
Homozygous LoFs: 0
Heterozygous LoFs: 18
Defined: 125745
p: 0.0000716

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.831	288	331	0.871	0.0000171	4149
Missense (PolyPhen)		134	165.1	0.81163		2032
Synonymous	0.477	123	130	0.947	0.00000651	1306
Loss of Function	2.64	8	21.1	0.380	0.00000114	269

Population LoF Frequency

Population	CAF	p-value	Status
African	0	0.0	absent
Latino/Admixed American	0.000040	0.000029	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0.00012	0.00011	rare
Finnish	0.000046	0.000046	rare
European (Non-Finnish)	0.00010	0.000097	rare
South Asian	0.00011	0.000098	rare
Other	0	0.0	absent

dbNSFP Gene Annotations

Source: dbNSFP

Recessive Scores

pRec: 0.110

Intolerance Scores

LoFtool: 0.621
RVIS EVS: -0.07
RVIS percentile EVS: 48.69

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: E
Indispensability score: 0.893

Gene Damage Prediction

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