ANKS1A

ankyrin repeat and sterile alpha motif domain containing 1A, the group of Ankyrin repeat domain containing|Sterile alpha motif domain containing

Basic information

Region (hg38): 6:34889254-35091406

Previous symbols: [ "ANKS1" ]

Links

ENSG00000064999 ∙ NCBI:23294 ∙ OMIM:608994 ∙ HGNC:20961 ∙ Uniprot:Q92625 ∙ 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 ANKS1A gene.

• Inborn genetic diseases (45 variants)
• not provided (9 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ANKS1A 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				2	2	4
missense			41	3	2	46
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region				2	1	3
non coding					1	1
Total	0	0	41	5	5

Variants in ANKS1A

This is a list of pathogenic ClinVar variants found in the ANKS1A region.

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

Position	Type	Phenotype	Significance	ClinVar
6-34889406-G-A		not specified	Uncertain significance (Dec 19, 2022)
6-34889581-C-T		not specified	Uncertain significance (Dec 12, 2023)
6-34967239-C-T		not specified	Likely benign (Jun 16, 2023)
6-34967290-C-G			Likely benign (Mar 01, 2024)
6-34970052-C-T			Likely benign (Jan 12, 2018)
6-34970074-T-C		not specified	Uncertain significance (Aug 10, 2023)
6-34981799-T-G		not specified	Uncertain significance (Apr 18, 2023)
6-34981854-G-A		not specified	Uncertain significance (Nov 02, 2023)
6-34981954-C-A		not specified	Uncertain significance (Jul 06, 2021)
6-34982758-A-G		not specified	Uncertain significance (Dec 09, 2023)
6-34983365-A-C		not specified	Uncertain significance (Aug 13, 2021)
6-34983414-A-G		not specified	Uncertain significance (Jan 09, 2023)
6-34985204-G-A		not specified	Uncertain significance (Feb 07, 2023)
6-34989233-C-T		not specified	Uncertain significance (Mar 29, 2022)
6-34994378-C-G		not specified	Uncertain significance (Jul 11, 2023)
6-34994416-A-G			Benign (Jul 18, 2018)
6-35017465-A-G			Likely benign (Dec 31, 2019)
6-35017481-C-T		not specified	Uncertain significance (Dec 01, 2022)
6-35017482-G-A		not specified	Uncertain significance (Aug 12, 2021)
6-35017512-C-T		not specified	Uncertain significance (Aug 09, 2021)
6-35017563-G-A		not specified	Uncertain significance (Dec 16, 2023)
6-35017580-G-A		not specified	Uncertain significance (Jun 12, 2023)
6-35017616-G-A		not specified	Likely benign (Jul 21, 2021)
6-35017616-G-C		not specified	Likely benign (Aug 19, 2021)
6-35017628-C-T		not specified	Uncertain significance (Sep 06, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ANKS1A	protein_coding	protein_coding	ENST00000360359	24	202138

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.809	0.191	125729	0	19	125748	0.0000756

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.81	452	655	0.691	0.0000396	7370
Missense in Polyphen		125	246.68	0.50674		2792
Synonymous	0.858	259	277	0.934	0.0000183	2288
Loss of Function	5.42	11	53.9	0.204	0.00000272	628

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000119	0.000119
Ashkenazi Jewish	0.000496	0.000496
East Asian	0.0000561	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.0000707	0.0000703
Middle Eastern	0.0000561	0.0000544
South Asian	0.0000658	0.0000653
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Regulator of different signaling pathways. Regulates EPHA8 receptor tyrosine kinase signaling to control cell migration and neurite retraction (By similarity). {ECO:0000250, ECO:0000269|PubMed:17875921}.
• Pathway: EGFR1 (Consensus)

Recessive Scores

• pRec: 0.116

Intolerance Scores

• loftool: 0.396
• rvis_EVS: -1.25
• rvis_percentile_EVS: 5.36

Haploinsufficiency Scores

• pHI: 0.447
• hipred: Y
• hipred_score: 0.597
• ghis: 0.530

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.987

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Anks1
• Phenotype: normal phenotype

Gene ontology

• Biological process: substrate-dependent cell migration;neuron remodeling;ephrin receptor signaling pathway;regulation of ephrin receptor signaling pathway
• Cellular component: nucleoplasm;cytosol;neuron projection
• Molecular function: protein binding;ephrin receptor binding