ANKRD53

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

Basic information

Region (hg38): 2:70978379-70985499

Links

ENSG00000144031 ∙ NCBI:79998 ∙ OMIM:617009 ∙ HGNC:25691 ∙ Uniprot:Q8N9V6 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the ANKRD53 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ANKRD53 gene is commonly pathogenic or not.

In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.

Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.

Variant type	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous				3		3
missense			45	4		49
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	45	7	0

Variants in ANKRD53

This is a list of pathogenic ClinVar variants found in the ANKRD53 region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
2-70978671-G-A		not specified	Uncertain significance (Apr 25, 2023)
2-70978677-C-A		not specified	Uncertain significance (Jan 26, 2022)
2-70978779-A-T		not specified	Uncertain significance (Oct 27, 2022)
2-70978793-G-A		not specified	Uncertain significance (Sep 27, 2022)
2-70979154-G-T		not specified	Uncertain significance (Sep 21, 2023)
2-70979156-C-A		not specified	Uncertain significance (Dec 11, 2023)
2-70979188-G-T		not specified	Uncertain significance (Aug 16, 2022)
2-70979189-C-T		not specified	Likely benign (Aug 16, 2022)
2-70979206-A-G		not specified	Likely benign (Mar 01, 2024)
2-70979208-G-C		not specified	Uncertain significance (Oct 05, 2023)
2-70979254-T-G		not specified	Uncertain significance (Sep 27, 2021)
2-70979671-C-A		not specified	Uncertain significance (Jun 09, 2022)
2-70979680-T-A		not specified	Uncertain significance (Oct 26, 2022)
2-70979721-G-A		not specified	Uncertain significance (Oct 06, 2021)
2-70979757-A-C		not specified	Uncertain significance (Jun 12, 2023)
2-70979770-C-T		not specified	Uncertain significance (May 15, 2024)
2-70979781-C-T		not specified	Uncertain significance (Apr 23, 2024)
2-70979800-A-C		not specified	Uncertain significance (Mar 19, 2024)
2-70981947-A-G		not specified	Uncertain significance (Mar 06, 2023)
2-70981956-C-T		not specified	Uncertain significance (Jun 10, 2024)
2-70981976-C-T		not specified	Uncertain significance (Oct 03, 2023)
2-70982001-A-C		not specified	Uncertain significance (Jul 06, 2021)
2-70982099-C-T		not specified	Uncertain significance (Dec 03, 2021)
2-70982583-G-A			Likely benign (Jul 01, 2022)
2-70982595-G-A		not specified	Uncertain significance (Aug 12, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ANKRD53	protein_coding	protein_coding	ENST00000360589	6	7117

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
4.09e-7	0.379	125633	0	115	125748	0.000457

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.482	288	312	0.923	0.0000169	3435
Missense in 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

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00153	0.00137
Ashkenazi Jewish	0.00	0.00
East Asian	0.000881	0.000761
Finnish	0.00	0.00
European (Non-Finnish)	0.000224	0.000220
Middle Eastern	0.000881	0.000761
South Asian	0.00137	0.00137
Other	0.000668	0.000652

dbNSFP

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

Haploinsufficiency Scores

• pHI: 0.0666
• hipred: N
• hipred_score: 0.153
• ghis: 0.444

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.501

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Ankrd53
• Phenotype: hearing/vestibular/ear phenotype

Gene ontology

• Biological process: mitotic metaphase plate congression;positive regulation of microtubule polymerization;cell division;regulation of mitotic spindle organization;regulation of mitotic cytokinesis
• Cellular component: spindle pole;cytoplasm;spindle
• Molecular function: protein binding