KANK3

protein-coding

KN motif and ankyrin repeat domains 3, the group of KN motif and ankyrin repeat domain containing

Gene summary

Predicted to be involved in negative regulation of actin filament polymerization. Predicted to be active in cytoplasm and cytoskeleton. [provided by Alliance of Genome Resources, Jul 2025]

Previous symbols:

ANKRD47

MANE transcript

NM_198471.3

Inheritance

—

ClinVar variants

U:154B:10

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.68

Max pathogenic AF

—

Genomic locus

chr19:8,322,584-8,343,262

External References & Databases

Ensembl (ENSG00000186994)

Transcript & Mutation Effects

hg38 • Region Span ~20.7 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 KANK3 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 158

not providedTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_198471.3. 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	1 clinvar		3
missense			150 clinvar	9 clinvar		159
nonsense			1 clinvar			1
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			1 clinvar			1
Total	0	0	154	10	0	164

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 66 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_198471.3	RefSeq	NP_940873.2	10	MANE Select
ENST00000330915.7	Ensembl	ENSP00000328923.2	10	MANE Select
ENST00000593649.5	Ensembl	ENSP00000470728.1	10	Standard
ENST00000593649.6	Ensembl	ENSP00000470728.1	10	Standard

Model Organisms & Knockout Phenotypes

Observed phenotypic effects in mouse and zebrafish models

Gene / Model	Organism	Observed Phenotype
kank3	Danio rerio	Structure: epidermal cell Quality: increased variability of size abnormal

Gene / Model

Organism

Observed Phenotype

kank3

Danio rerio

Structure: epidermal cell

Quality: increased variability of size

abnormal

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

negative regulation of actin filament polymerization

Cellular Component

cytoplasm

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000330915
Coding exons: 10
Length: 20679
Individuals with no LoFs: 125706
Homozygous LoFs: 0
Heterozygous LoFs: 42
Defined: 125748
p: 0.000167

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.953	276	324	0.851	0.0000174	5055
Missense (PolyPhen)		57	73.533	0.77517		1680
Synonymous	-0.380	151	145	1.04	0.00000823	1820
Loss of Function	1.37	15	21.9	0.684	0.00000113	281

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00012	0.00012	rare
Latino/Admixed American	0.00023	0.00023	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0	0.0	absent
Finnish	0.000047	0.000046	rare
European (Non-Finnish)	0.00024	0.00024	rare
South Asian	0.000098	0.000098	rare
Other	0.00017	0.00016	rare

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: May be involved in the control of cytoskeleton formation by regulating actin polymerization.;

Recessive Scores

pRec: 0.0957

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.299

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	High	High	High
Primary Immunodeficiency	High	High	High
Cancer	High	High	High