ANKS3

protein-coding

ankyrin repeat and sterile alpha motif domain containing 3, the group of Sterile alpha motif domain containing|Ankyrin repeat domain containing

Gene summary

Predicted to be located in cytoplasm. Predicted to be active in cilium. [provided by Alliance of Genome Resources, Jul 2025]

MANE transcript

NM_133450.4

Inheritance

AD, AR

ClinVar variants

P:1U:160B:22

Top phenotype

situs inversus

gnomAD constraint

pLI —, LoF o/e 0.48

Max pathogenic AF

—

Genomic locus

chr16:4,696,510-4,734,378

External References & Databases

Ensembl (ENSG00000168096)

Transcript & Mutation Effects

hg38 • Region Span ~37.9 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

situs inversusSUPPORTIVE

Inheritance Pattern: AD

Disease ID:MONDO:0010029

Submitter: Orphanet

laterality defects, autosomal dominantLIMITED

Inheritance Pattern: AR

Disease ID:MONDO:0010991

Submitter: Ambry Genetics

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to ANKS3 variants in ClinVar

5 Conditions Cataloged

not specifiedTotal: 162

not providedTotal: 11

ANKS3-related disorderTotal: 3

Short statureTotal: 1

Non-immune hydrops fetalisTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_133450.4. 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	4 clinvar	3 clinvar	9
missense			155 clinvar	14 clinvar	1 clinvar	170
nonsense						0
start loss						0
frameshift	1 clinvar					1
splice donor/acceptor (+/-2bp)			3 clinvar			3
Total	1	0	160	18	4	183

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 77 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_133450.4	RefSeq	NP_597707.1	15	MANE Select
ENST00000304283.9	Ensembl	ENSP00000304586.4	15	MANE Select
NM_001242929.2	RefSeq	NP_001229858.1	13	Standard
NM_001308089.2	RefSeq	NP_001295018.1	13	Standard

Model Organisms & Knockout Phenotypes

Observed phenotypic effects in mouse and zebrafish models

Gene / Model	Organism	Observed Phenotype
anks3	Danio rerio	Structure: pronephric tubule Quality: cystic abnormal

Gene / Model

Organism

Observed Phenotype

anks3

Danio rerio

Structure: pronephric tubule

Quality: cystic

abnormal

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Molecular Function

protein binding

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000304283
Coding exons: 15
Length: 37867
Individuals with no LoFs: 125715
Homozygous LoFs: 0
Heterozygous LoFs: 33
Defined: 125748
p: 0.000131

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	-1.76	497	398	1.25	0.0000258	4213
Missense (PolyPhen)		150	159.54	0.94022		1706
Synonymous	-3.89	235	170	1.38	0.0000122	1286
Loss of Function	2.83	17	35.1	0.484	0.00000184	384

Population LoF Frequency

Population	CAF	p-value	Status
African	0	0.0	absent
Latino/Admixed American	0.00021	0.00020	rare
Ashkenazi Jewish	0.00061	0.00060	rare
East Asian	0.00012	0.00011	rare
Finnish	0.00024	0.00023	rare
European (Non-Finnish)	0.000089	0.000088	rare
South Asian	0.000098	0.000098	rare
Other	0	0.0	absent

dbNSFP Gene Annotations

Source: dbNSFP

Recessive Scores

pRec: 0.0991

Intolerance Scores

LoFtool: 0.617
RVIS EVS: 0.01
RVIS percentile EVS: 54.16

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.133

Gene Damage Prediction

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