ANKRD53

protein-coding

ankyrin repeat domain 53, the group of Ankyrin repeat domain containing

Gene summary

Involved in mitotic metaphase chromosome alignment; regulation of microtubule cytoskeleton organization; and regulation of mitotic cytokinesis. Located in spindle pole. [provided by Alliance of Genome Resources, Jul 2025]

MANE transcript

NM_001115116.2

Inheritance

—

ClinVar variants

U:102B:10

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.83

Max pathogenic AF

—

Genomic locus

chr2:70,978,380-70,985,499

External References & Databases

Ensembl (ENSG00000144031)

Transcript & Mutation Effects

hg38 • Region Span ~7.1 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 ANKRD53 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 107

not providedTotal: 3

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_001115116.2. 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			1 clinvar	3 clinvar		4
missense			100 clinvar	7 clinvar		107
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			1 clinvar			1
Total	0	0	102	10	0	112

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 17 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_001115116.2	RefSeq	NP_001108588.1	6	MANE Select
ENST00000360589.4	Ensembl	ENSP00000353796.3	6	MANE Select
NM_001369683.1	RefSeq	NP_001356612.1	6	Standard
NM_024933.4	RefSeq	NP_079209.3	7	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

mitotic metaphase plate congression
positive regulation of microtubule polymerization
cell division
regulation of mitotic spindle organization
regulation of mitotic cytokinesis

Molecular Function

protein binding

Cellular Component

spindle pole
cytoplasm
spindle

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000360589
Coding exons: 6
Length: 7117
Individuals with no LoFs: 125633
Homozygous LoFs: 0
Heterozygous LoFs: 115
Defined: 125748
p: 0.000457

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.482	288	312	0.923	0.0000169	3435
Missense (PolyPhen)		75	87.147	0.86061		985
Synonymous	0.811	119	131	0.910	0.00000753	1065
Loss of Function	0.589	11	13.3	0.826	7.10e-7	144

Population LoF Frequency

Population	CAF	p-value	Status
African	0.0011	0.00092	notable
Latino/Admixed American	0.00044	0.00043	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0.00088	0.00076	rare
Finnish	0	0.0	absent
European (Non-Finnish)	0.00022	0.00022	rare
South Asian	0.0014	0.0014	notable
Other	0.00067	0.00065	rare

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: Required for normal progression through mitosis. Involved in chromosome alignment and cytokinesis via regulation of microtubules polymerization. {ECO:0000269|PubMed:26820536}.;

Recessive Scores

pRec: 0.0936

Intolerance Scores

LoFtool: 0.781
RVIS EVS: 1.27
RVIS percentile EVS: 93.6

Essentials

Essential (CRISPR): N
Essential (CRISPR2): S
Essential (gene trap): N
Indispensability pred.: E
Indispensability score: 0.501

Gene Damage Prediction

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