CTTNBP2

protein-coding

cortactin binding protein 2, the group of Ankyrin repeat domain containing|STRIPAK complex

Gene summary

This gene encodes a protein with six ankyrin repeats and several proline-rich regions. A similar gene in rat interacts with a central regulator of the actin cytoskeleton. [provided by RefSeq, Jul 2008]

Previous symbols:

CORTBP2
C7orf8

MANE transcript

NM_033427.3

Inheritance

ClinVar variants

U:145B:28

Top phenotype

CTTNBP2-related disorder

gnomAD constraint

pLI —, LoF o/e 0.44

Max pathogenic AF

—

Genomic locus

chr7:117,710,651-117,874,139

External References & Databases

Ensembl (ENSG00000077063)

Transcript & Mutation Effects

hg38 • Region Span ~163.5 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

autism spectrum disorderLIMITED

Inheritance Pattern: AD

Disease ID:MONDO:0005258

Submitter: Ambry Genetics

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to CTTNBP2 variants in ClinVar

4 Conditions Cataloged

not specifiedTotal: 124

CTTNBP2-related disorderTotal: 38

not providedTotal: 9

Prostate cancerTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_033427.3. 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			2 clinvar	10 clinvar	2 clinvar	14
missense			138 clinvar	11 clinvar	4 clinvar	153
nonsense			1 clinvar			1
start loss						0
frameshift			2 clinvar	1 clinvar		3
splice donor/acceptor (+/-2bp)			2 clinvar			2
Total	0	0	145	22	6	173

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 23 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_033427.3	RefSeq	NP_219499.1	23	MANE Select
ENST00000160373.8	Ensembl	ENSP00000160373.3	23	MANE Select
NM_001363349.1	RefSeq	NP_001350278.1	23	Standard
NM_001363350.1	RefSeq	NP_001350279.1	19	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

brain development
regulation of modification of postsynaptic actin cytoskeleton

Molecular Function

SH3 domain binding

Cellular Component

cell cortex
synaptic vesicle
dendritic spine
postsynaptic actin cytoskeleton
glutamatergic synapse

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000160373
Coding exons: 23
Length: 163489
Individuals with no LoFs: 125639
Homozygous LoFs: 0
Heterozygous LoFs: 109
Defined: 125748
p: 0.000434

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.651	833	888	0.939	0.0000473	10864
Missense (PolyPhen)		240	278.7	0.86113		3488
Synonymous	0.117	336	339	0.992	0.0000193	3328
Loss of Function	4.23	30	67.6	0.444	0.00000333	866

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00074	0.00074	rare
Latino/Admixed American	0.00050	0.00049	rare
Ashkenazi Jewish	0.00021	0.00020	rare
East Asian	0.0015	0.0015	notable
Finnish	0.000046	0.000046	rare
European (Non-Finnish)	0.00029	0.00029	rare
South Asian	0.00046	0.00046	rare
Other	0.00049	0.00049	rare

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: Regulates the dendritic spine distribution of CTTN/cortactin in hippocampal neurons, thus controls dendritic spinogenesis and dendritic spine maintenance. {ECO:0000250}.;

Recessive Scores

pRec: 0.124

Intolerance Scores

RVIS EVS: -1.45
RVIS percentile EVS: 3.9

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: E
Indispensability score: 0.622

Gene Damage Prediction

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