ANKS1B

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

Basic information

Region (hg38): 12:98726456-99984936

Links

ENSG00000185046 ∙ NCBI:56899 ∙ OMIM:607815 ∙ HGNC:24600 ∙ Uniprot:Q7Z6G8 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• complex neurodevelopmental disorder (Limited), mode of inheritance: AD
• complex neurodevelopmental disorder (Moderate), mode of inheritance: AD

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the ANKS1B gene.

• Inborn genetic diseases (34 variants)
• not provided (23 variants)
• Normal pregnancy (1 variants)
• not specified (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ANKS1B 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				5	5	10
missense			30	4	2	36
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)		1	1			2
splice region						0
non coding			4	2	2	8
Total	0	1	35	11	9

Variants in ANKS1B

This is a list of pathogenic ClinVar variants found in the ANKS1B region.

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

Position	Type	Phenotype	Significance	ClinVar
12-98727166-T-C		APAF1-related disorder	Likely benign (May 28, 2019)
12-98732429-G-A		not specified	Uncertain significance (Dec 03, 2021)
12-98732569-T-C		APAF1-related disorder	Benign (Jul 11, 2019)
12-98735616-G-A			Uncertain significance (Jun 06, 2021)
12-98745774-C-T			Likely benign (Jun 20, 2018)
12-98751357-C-T		not specified	Uncertain significance (Nov 13, 2023)
12-98751398-G-C		not specified	Uncertain significance (Feb 26, 2024)
12-98773176-T-C		not specified	Uncertain significance (Oct 04, 2022)
12-98773181-T-C		not specified	Uncertain significance (Sep 27, 2022)
12-98781115-A-G			Likely pathogenic (Feb 19, 2020)
12-98798993-T-C		not specified	Uncertain significance (Nov 12, 2021)
12-98801071-C-T		not specified	Uncertain significance (Jun 01, 2023)
12-98801073-G-A		not specified	Uncertain significance (Oct 12, 2022)
12-98829259-A-C		not specified	Uncertain significance (Oct 13, 2021)
12-98829260-T-C		not specified	Uncertain significance (Jan 19, 2024)
12-98829332-G-A		not specified	Uncertain significance (May 26, 2022)
12-98832070-C-T		not specified	Uncertain significance (Aug 15, 2023)
12-99053161-A-G		not specified	Uncertain significance (Nov 13, 2023)
12-99053272-G-A		not specified	Uncertain significance (Nov 15, 2023)
12-99084952-A-C		not specified	Uncertain significance (Sep 14, 2022)
12-99084970-A-G			Likely benign (Dec 31, 2019)
12-99085016-T-C		not specified	Uncertain significance (May 23, 2023)
12-99154346-C-T			Benign (Dec 31, 2019)
12-99154454-G-A			Benign (Dec 31, 2019)
12-99244388-A-C		not specified	Uncertain significance (Jun 18, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ANKS1B	protein_coding	protein_coding	ENST00000547776	26	1258198

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.00	0.0000218	124624	0	11	124635	0.0000441

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.95	432	642	0.673	0.0000320	8139
Missense in Polyphen		74	193.06	0.38329		2446
Synonymous	0.292	239	245	0.976	0.0000134	2416
Loss of Function	6.41	7	61.1	0.115	0.00000317	774

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000119	0.000119
Ashkenazi Jewish	0.000200	0.000199
East Asian	0.00	0.00
Finnish	0.0000465	0.0000464
European (Non-Finnish)	0.0000277	0.0000265
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.000165	0.000165

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Isoform 2 may participate in the regulation of nucleoplasmic coilin protein interactions in neuronal and transformed cells.; FUNCTION: Isoform 4 may play a role as a modulator of APP processing. Overexpression can down-regulate APP processing.
• Pathway: Ectoderm Differentiation (Consensus)

Recessive Scores

• pRec: 0.210

Intolerance Scores

• loftool: 0.269
• rvis_EVS: -1.22
• rvis_percentile_EVS: 5.67

Haploinsufficiency Scores

• pHI: 0.212
• hipred: Y
• hipred_score: 0.508
• ghis: 0.584

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.595

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Anks1b
• Phenotype: skeleton phenotype; nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan); mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); homeostasis/metabolism phenotype; adipose tissue phenotype (the observable morphological and physiological characteristics of mammalian fat tissue that are manifested through development and lifespan)

Gene ontology

• Biological process: regulation of synaptic plasticity by receptor localization to synapse
• Cellular component: cytosol;plasma membrane;postsynaptic density;Cajal body;cell junction;dendritic spine;intracellular membrane-bounded organelle;postsynaptic membrane
• Molecular function: ephrin receptor binding