ANKMY1

ankyrin repeat and MYND domain containing 1, the group of Ankyrin repeat domain containing|Zinc fingers MYND-type

Basic information

Region (hg38): 2:240479421-240569209

Links

ENSG00000144504 ∙ NCBI:51281 ∙ ∙ HGNC:20987 ∙ Uniprot:Q9P2S6 ∙ 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 ANKMY1 gene.

• Inborn genetic diseases (71 variants)
• not provided (6 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ANKMY1 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	3	4
missense			55	8	1	64
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding			9			9
Total	0	0	64	9	4

Variants in ANKMY1

This is a list of pathogenic ClinVar variants found in the ANKMY1 region.

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

Position	Type	Phenotype	Significance	ClinVar
2-240479638-C-T		not specified	Uncertain significance (Feb 10, 2022)
2-240479650-G-T		not specified	Uncertain significance (May 23, 2023)
2-240480956-G-A			Likely benign (Apr 01, 2023)
2-240481021-C-T		not specified	Uncertain significance (Feb 06, 2024)
2-240481032-G-A		not specified	Uncertain significance (May 27, 2022)
2-240481048-G-A		not specified	Uncertain significance (Jan 19, 2024)
2-240481062-C-G		not specified	Uncertain significance (Jun 30, 2022)
2-240482261-G-A		not specified	Likely benign (Feb 10, 2023)
2-240500020-C-T		not specified	Uncertain significance (May 30, 2023)
2-240500051-G-A		not specified	Uncertain significance (Jan 10, 2022)
2-240500056-C-T		not specified	Uncertain significance (Mar 21, 2023)
2-240500075-G-A		not specified	Uncertain significance (Dec 12, 2022)
2-240500085-C-T		not specified	Uncertain significance (Nov 19, 2022)
2-240500474-T-C		not specified	Uncertain significance (Dec 17, 2023)
2-240500475-A-C		not specified	Uncertain significance (Apr 28, 2022)
2-240500538-C-T		not specified	Uncertain significance (Apr 12, 2022)
2-240500539-G-A			Benign (Jun 05, 2018)
2-240507580-T-C		not specified	Likely benign (Jun 24, 2022)
2-240507618-C-T		not specified	Uncertain significance (Jan 30, 2024)
2-240507691-C-T		not specified	Likely benign (Mar 06, 2023)
2-240509367-A-G		not specified	Uncertain significance (Feb 06, 2023)
2-240509391-C-T		not specified	Uncertain significance (Sep 01, 2021)
2-240509419-C-T		not specified	Likely benign (Dec 19, 2022)
2-240509436-C-T		not specified	Likely benign (Dec 27, 2023)
2-240509439-A-G		not specified	Uncertain significance (Jul 14, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ANKMY1	protein_coding	protein_coding	ENST00000391987	16	89788

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
2.63e-24	0.00166	125401	0	347	125748	0.00138

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.257	587	570	1.03	0.0000348	6165
Missense in Polyphen		205	200.76	1.0211		2149
Synonymous	0.0389	247	248	0.997	0.0000168	1852
Loss of Function	0.440	38	41.0	0.926	0.00000201	478

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00311	0.00311
Ashkenazi Jewish	0.00179	0.00179
East Asian	0.00315	0.00316
Finnish	0.000139	0.000139
European (Non-Finnish)	0.00111	0.00110
Middle Eastern	0.00315	0.00316
South Asian	0.00262	0.00262
Other	0.00117	0.00114

dbNSFP

Source: dbNSFP

Intolerance Scores

• loftool: 0.930
• rvis_EVS: -0.23
• rvis_percentile_EVS: 37.13

Haploinsufficiency Scores

• pHI: 0.0864
• hipred: N
• hipred_score: 0.180
• ghis: 0.546

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.147

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Ankmy1

Gene ontology

• Molecular function: metal ion binding