ANKRD39

ankyrin repeat domain 39, the group of Ankyrin repeat domain containing

Basic information

Region (hg38): 2:96836611-96858016

Links

ENSG00000213337 ∙ NCBI:51239 ∙ ∙ HGNC:28640 ∙ Uniprot:Q53RE8 ∙ 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 ANKRD39 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ANKRD39 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			19			19
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	19	0	0

Variants in ANKRD39

This is a list of pathogenic ClinVar variants found in the ANKRD39 region.

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

Position	Type	Phenotype	Significance	ClinVar
2-96839562-C-T		not specified	Uncertain significance (Apr 06, 2024)
2-96839595-C-G		not specified	Uncertain significance (Oct 05, 2023)
2-96839608-G-T		not specified	Uncertain significance (Jan 23, 2023)
2-96839641-A-G		not specified	Uncertain significance (Mar 18, 2024)
2-96839755-T-G		not specified	Uncertain significance (Apr 12, 2022)
2-96839780-T-G		not specified	Uncertain significance (Feb 05, 2024)
2-96839785-C-A		not specified	Uncertain significance (Jun 24, 2022)
2-96840008-C-T		not specified	Uncertain significance (Dec 27, 2022)
2-96840050-C-T		not specified	Uncertain significance (Oct 06, 2022)
2-96840251-C-T		not specified	Likely benign (Nov 10, 2022)
2-96840426-G-A		not specified	Uncertain significance (Jun 11, 2024)
2-96840427-C-T		not specified	Uncertain significance (Mar 14, 2023)
2-96840441-C-A		not specified	Uncertain significance (Feb 23, 2023)
2-96840445-C-A		not specified	Uncertain significance (Dec 06, 2021)
2-96840508-G-A		not specified	Uncertain significance (Nov 17, 2023)
2-96840792-C-A		not specified	Uncertain significance (Feb 28, 2023)
2-96840813-C-T		not specified	Uncertain significance (Mar 06, 2023)
2-96840845-T-G		not specified	Uncertain significance (Feb 28, 2023)
2-96842121-T-A		not specified	Uncertain significance (Jan 24, 2024)
2-96842175-A-C		not specified	Uncertain significance (Oct 26, 2021)
2-96842178-C-G		not specified	Uncertain significance (Apr 08, 2022)
2-96842479-C-G		not specified	Uncertain significance (Nov 17, 2023)
2-96848320-C-T		not specified	Uncertain significance (Feb 23, 2023)
2-96848339-G-A		not specified	Uncertain significance (Oct 02, 2023)
2-96848353-G-C		not specified	Uncertain significance (Mar 30, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ANKRD39	protein_coding	protein_coding	ENST00000393537	4	21485

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.000902	0.813	125729	0	17	125746	0.0000676

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.181	112	118	0.953	0.00000730	1155
Missense in Polyphen		33	47.879	0.68923		449
Synonymous	0.809	46	53.5	0.859	0.00000349	385
Loss of Function	1.13	6	9.81	0.611	6.76e-7	84

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000564	0.000546
Ashkenazi Jewish	0.00	0.00
East Asian	0.000109	0.000109
Finnish	0.00	0.00
European (Non-Finnish)	0.0000283	0.0000264
Middle Eastern	0.000109	0.000109
South Asian	0.0000327	0.0000327
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Intolerance Scores

• loftool: 0.604
• rvis_EVS: -0.14
• rvis_percentile_EVS: 43.29

Haploinsufficiency Scores

• pHI: 0.267
• hipred: N
• hipred_score: 0.170
• ghis: 0.547

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.874

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Ankrd39

Gene ontology

• Biological process: biological_process
• Cellular component: cellular_component
• Molecular function: molecular_function