ANKHD1

ankyrin repeat and KH domain containing 1, the group of Ankyrin repeat domain containing

Basic information

Region (hg38): 5:140401813-140539856

Links

ENSG00000131503 ∙ NCBI:54882 ∙ OMIM:610500 ∙ HGNC:24714 ∙ Uniprot:Q8IWZ3 ∙ 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 ANKHD1 gene.

• not provided (4 variants)
• Inborn genetic diseases (4 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ANKHD1 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				1		1
missense			4		1	5
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding					1	1
Total	0	0	4	1	2

Variants in ANKHD1

This is a list of pathogenic ClinVar variants found in the ANKHD1 region.

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

Position	Type	Phenotype	Significance	ClinVar
5-140438518-G-A		not specified	Uncertain significance (Jan 10, 2022)
5-140458755-T-C		not specified	Uncertain significance (Feb 12, 2024)
5-140459273-T-C			Likely benign (Feb 01, 2023)
5-140485620-A-G		not specified	Uncertain significance (Jan 23, 2024)
5-140507254-A-G			Benign (Oct 21, 2019)
5-140509694-G-A		not specified	Uncertain significance (Dec 12, 2023)
5-140526166-C-T		not specified	Uncertain significance (Jan 05, 2022)
5-140528334-A-AG			not provided (-)
5-140529615-AGCTAACCAGG-A			Uncertain significance (Feb 01, 2024)
5-140529737-A-G		not specified	Uncertain significance (Nov 07, 2022)
5-140537517-C-G			Benign (Apr 05, 2018)
5-140539380-C-T		not specified	Uncertain significance (Apr 07, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ANKHD1	protein_coding	protein_coding	ENST00000297183	36	147765

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.00	2.14e-13	124478	1	48	124527	0.000197

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	4.47	886	1.35e+3	0.657	0.0000681	16924
Missense in Polyphen		135	253.3	0.53297		3146
Synonymous	0.941	468	495	0.946	0.0000253	5461
Loss of Function	9.00	6	106	0.0566	0.00000597	1311

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00126	0.00126
Ashkenazi Jewish	0.00	0.00
East Asian	0.000109	0.000109
Finnish	0.0000462	0.0000462
European (Non-Finnish)	0.0000274	0.0000269
Middle Eastern	0.000109	0.000109
South Asian	0.000163	0.0000980
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May play a role as a scaffolding protein that may be associated with the abnormal phenotype of leukemia cells. Isoform 2 may possess an antiapoptotic effect and protect cells during normal cell survival through its regulation of caspases. {ECO:0000269|PubMed:16098192}.

Recessive Scores

• pRec: 0.112

Intolerance Scores

• loftool: 0.407
• rvis_EVS: -2.36
• rvis_percentile_EVS: 1.14

Haploinsufficiency Scores

• hipred: N
• hipred_score: 0.455
• ghis: 0.528

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: H
• gene_indispensability_pred: E
• gene_indispensability_score: 0.991

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Ankhd1

Zebrafish Information Network

• Gene name: ankhd1
• Affected structure: atrium
• Phenotype tag: abnormal
• Phenotype quality: dilated

Gene ontology

• Biological process: innate immune response
• Cellular component: cytoplasm
• Molecular function: RNA binding;protein binding