ANKHD1-EIF4EBP3

ANKHD1-EIF4EBP3 readthrough

Basic information

Region (hg38): 5:140401908-140549569

Links

ENSG00000254996 ∙ NCBI:404734 ∙ ∙ HGNC:33530 ∙ ∙ ∙ 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-EIF4EBP3 gene.

• Inborn genetic diseases (15 variants)
• not provided (4 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ANKHD1-EIF4EBP3 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	2		5
missense			9		1	10
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding			2		1	3
Total	0	0	14	2	2

Variants in ANKHD1-EIF4EBP3

This is a list of pathogenic ClinVar variants found in the ANKHD1-EIF4EBP3 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 (Nov 13, 2024)
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)
5-140537578-A-G		not specified	Uncertain significance (Sep 05, 2024)
5-140539380-C-T		not specified	Uncertain significance (Apr 07, 2023)
5-140542185-C-T		not specified	Uncertain significance (Jun 11, 2021)
5-140542191-T-G		not specified	Uncertain significance (Jul 16, 2024)
5-140542220-C-A		not specified	Uncertain significance (Oct 10, 2023)
5-140542220-C-G		not specified	Uncertain significance (Mar 16, 2022)
5-140542230-C-G		not specified	Uncertain significance (Oct 03, 2024)
5-140542238-A-G		not specified	Uncertain significance (Sep 20, 2023)
5-140542253-C-T		not specified	Uncertain significance (Aug 12, 2021)
5-140547801-A-C		not specified	Uncertain significance (Apr 13, 2022)
5-140548907-C-A		not specified	Uncertain significance (Feb 28, 2024)
5-140548919-C-G		EBV-positive nodal T- and NK-cell lymphoma	Likely benign (-)
5-140548926-C-T		not specified	Uncertain significance (Jan 04, 2024)
5-140548927-G-A		not specified	Uncertain significance (Aug 10, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ANKHD1-EIF4EBP3	protein_coding	protein_coding	ENST00000532219	36	147662

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}.

Intolerance Scores

• rvis_EVS: -2.53
• rvis_percentile_EVS: 0.89

Haploinsufficiency Scores

• hipred: N
• hipred_score: 0.455
• ghis: 0.504

Essentials

• essential_gene_CRISPR: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.933