ANKRD6

protein-coding

ankyrin repeat domain 6, the group of Ankyrin repeat domain containing

Gene summary

Predicted to be involved in establishment or maintenance of cell polarity and regulation of Wnt signaling pathway. Predicted to act upstream of or within negative regulation of canonical Wnt signaling pathway and positive regulation of Wnt signaling pathway, planar cell polarity pathway. Predicted to be located in cytoplasm and nucleus. [provided by Alliance of Genome Resources, Jun 2026]

MANE transcript

NM_001242809.2

Inheritance

—

ClinVar variants

U:126B:13

Top phenotype

ANKRD6-related disorder

gnomAD constraint

pLI —, LoF o/e 0.64

Max pathogenic AF

—

Genomic locus

chr6:89,433,152-89,633,834

External References & Databases

Ensembl (ENSG00000135299)

Transcript & Mutation Effects

hg38 • Region Span ~200.7 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 ANKRD6 variants in ClinVar

3 Conditions Cataloged

not specifiedTotal: 118

not providedTotal: 7

ANKRD6-related disorderTotal: 5

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_001242809.2. 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			4 clinvar	4 clinvar	3 clinvar	11
missense			119 clinvar	4 clinvar	2 clinvar	125
nonsense			2 clinvar			2
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			1 clinvar			1
Total	0	0	126	8	5	139

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 186 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_001242809.2	RefSeq	NP_001229738.1	15	MANE Select
ENST00000339746.9	Ensembl	ENSP00000345767.4	15	MANE Select
NM_001242811.1	RefSeq	NP_001229740.1	15	Standard
NM_001242813.1	RefSeq	NP_001229742.1	14	Standard

Model Organisms & Knockout Phenotypes

Observed phenotypic effects in mouse and zebrafish models

Gene / Model	Organism	Observed Phenotype
ankrd6b	Danio rerio	Structure: whole organism Quality: decreased length abnormal

Gene / Model

Organism

Observed Phenotype

ankrd6b

Danio rerio

Structure: whole organism

Quality: decreased length

abnormal

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

positive regulation of JNK cascade
negative regulation of canonical Wnt signaling pathway
positive regulation of Wnt signaling pathway, planar cell polarity pathway

Cellular Component

nucleus
cytoplasm
intracellular membrane-bounded organelle

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000522441
Coding exons: 15
Length: 200665
Individuals with no LoFs: 124591
Homozygous LoFs: 0
Heterozygous LoFs: 61
Defined: 124652
p: 0.000245

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.742	364	406	0.896	0.0000228	4673
Missense (PolyPhen)		110	124.95	0.88038		1469
Synonymous	0.954	149	165	0.905	0.0000100	1440
Loss of Function	2.00	23	35.9	0.641	0.00000195	414

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00019	0.00019	rare
Latino/Admixed American	0.00050	0.00049	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0.00045	0.00044	rare
Finnish	0	0.0	absent
European (Non-Finnish)	0.00023	0.00023	rare
South Asian	0.00020	0.00020	rare
Other	0.00017	0.00017	rare

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: Recruits CKI-epsilon to the beta-catenin degradation complex that consists of AXN1 or AXN2 and GSK3-beta and allows efficient phosphorylation of beta-catenin, thereby inhibiting beta-catenin/Tcf signals. {ECO:0000250}.;

Recessive Scores

pRec: 0.110

Intolerance Scores

LoFtool: 0.920
RVIS EVS: 0.07
RVIS percentile EVS: 59.16

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: E
Indispensability score: 0.823

Gene Damage Prediction

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