ANKRD28

protein-coding

ankyrin repeat domain 28, the group of Cilia and flagella associated|Ankyrin repeat domain containing|MicroRNA protein coding host genes|Protein phosphatase 1 regulatory subunits|Protein phosphatase 6 regulatory subunits

Gene summary

Enables protein phosphatase regulator activity. Involved in positive regulation of focal adhesion assembly. Located in cytosol and lamellipodium. Part of protein serine/threonine phosphatase complex. [provided by Alliance of Genome Resources, Jun 2026]

MANE transcript

NM_001349278.2

Inheritance

—

ClinVar variants

U:156B:11

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.07

Max pathogenic AF

—

Genomic locus

chr3:15,667,236-15,859,771

External References & Databases

Ensembl (ENSG00000206560)

Transcript & Mutation Effects

hg38 • Region Span ~192.5 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 ANKRD28 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 139

not providedTotal: 14

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_001349278.2. 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			2 clinvar	9 clinvar		11
missense			148 clinvar	2 clinvar		150
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			6 clinvar			6
Total	0	0	156	11	0	167

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 43 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_001349278.2	RefSeq	NP_001336207.1	28	MANE Select
ENST00000683139.1	Ensembl	ENSP00000508086.1	28	MANE Select
NM_001195098.1	RefSeq	NP_001182027.1	23	Standard
NM_001195099.2	RefSeq	NP_001182028.1	23	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

Vesicle-mediated transport
Membrane Trafficking
Post-translational protein modification
Metabolism of proteins
Transport to the Golgi and subsequent modification

Biological Process

COPII vesicle coating

Molecular Function

protein binding

Cellular Component

Golgi membrane
nucleoplasm
cytosol

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000399451
Coding exons: 28
Length: 192536
Individuals with no LoFs: 124626
Homozygous LoFs: 0
Heterozygous LoFs: 10
Defined: 124636
p: 0.0000401

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	2.39	390	547	0.713	0.0000271	6833
Missense (PolyPhen)		117	207.22	0.56462		2583
Synonymous	1.28	178	201	0.885	0.0000107	2024
Loss of Function	6.27	4	53.5	0.0747	0.00000280	697

Population LoF Frequency

Population	CAF	p-value	Status
African	0.000065	0.000065	rare
Latino/Admixed American	0	0.0	absent
Ashkenazi Jewish	0	0.0	absent
East Asian	0	0.0	absent
Finnish	0.00019	0.00019	rare
European (Non-Finnish)	0.000044	0.000044	rare
South Asian	0	0.0	absent
Other	0	0.0	absent

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: Putative regulatory subunit of protein phosphatase 6 (PP6) that may be involved in the recognition of phosphoprotein substrates. Involved in the PP6-mediated dephosphorylation of NFKBIE opposing its degradation in response to TNF-alpha. Selectively inhibits the phosphatase activity of PPP1C. Targets PPP1C to modulate HNRPK phosphorylation. {ECO:0000269|PubMed:16564677, ECO:0000269|PubMed:18186651}.;

Recessive Scores

pRec: 0.0968

Intolerance Scores

RVIS EVS: -0.8
RVIS percentile EVS: 12.49

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: E
Indispensability score: 0.708

Gene Damage Prediction

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