ANKRA2

ankyrin repeat family A member 2, the group of Ankyrin repeat domain containing

Basic information

Region (hg38): 5:73552190-73565667

Links

ENSG00000164331 ∙ NCBI:57763 ∙ OMIM:605787 ∙ HGNC:13208 ∙ Uniprot:Q9H9E1 ∙ 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 ANKRA2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ANKRA2 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						0
missense			12			12
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	12	0	0

Variants in ANKRA2

This is a list of pathogenic ClinVar variants found in the ANKRA2 region.

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

Position	Type	Phenotype	Significance	ClinVar
5-73552834-G-A		not specified	Uncertain significance (Mar 29, 2023)
5-73554940-G-A		not specified	Uncertain significance (Apr 24, 2024)
5-73554977-G-T		not specified	Uncertain significance (Dec 11, 2023)
5-73555505-C-G		not specified	Uncertain significance (Aug 30, 2022)
5-73561228-G-C		not specified	Uncertain significance (Dec 13, 2023)
5-73561240-T-C		not specified	Uncertain significance (Apr 01, 2024)
5-73561247-C-G		not specified	Uncertain significance (Feb 10, 2022)
5-73561258-G-A		not specified	Uncertain significance (May 02, 2024)
5-73561268-A-T		not specified	Uncertain significance (Dec 14, 2023)
5-73561281-G-C		not specified	Uncertain significance (Oct 27, 2023)
5-73562674-T-G		not specified	Uncertain significance (Mar 07, 2024)
5-73562710-T-C		not specified	Uncertain significance (May 09, 2023)
5-73562737-C-T		not specified	Uncertain significance (Nov 13, 2023)
5-73562787-A-G		not specified	Uncertain significance (Apr 04, 2023)
5-73562822-G-T		not specified	Uncertain significance (Feb 16, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ANKRA2	protein_coding	protein_coding	ENST00000296785	8	13352

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00000354	0.818	125709	0	38	125747	0.000151

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.825	136	166	0.820	0.00000783	2044
Missense in Polyphen		57	90.931	0.62685		1130
Synonymous	0.633	55	61.3	0.897	0.00000313	614
Loss of Function	1.35	11	17.0	0.646	9.38e-7	199

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000268	0.000268
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.000238	0.000237
Middle Eastern	0.00	0.00
South Asian	0.000131	0.000131
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May regulate the interaction between the 3M complex and the histone deacetylases HDAC4 and HDAC5 (PubMed:25752541). May also regulate LRP2/megalin (By similarity). {ECO:0000250|UniProtKB:A2ARV4, ECO:0000269|PubMed:25752541}.
• Pathway: Signaling events mediated by HDAC Class II (Consensus)

Recessive Scores

• pRec: 0.121

Intolerance Scores

• loftool: 0.737
• rvis_EVS: -0.32
• rvis_percentile_EVS: 31.46

Haploinsufficiency Scores

• pHI: 0.398
• hipred: Y
• hipred_score: 0.765
• ghis: 0.656

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.773

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Ankra2

Gene ontology

• Biological process: regulation of protein complex assembly
• Cellular component: nucleus;cytosol;cytoskeleton;membrane;protein-containing complex;3M complex
• Molecular function: protein binding;protein kinase binding;ubiquitin protein ligase binding;histone deacetylase binding;low-density lipoprotein particle receptor binding