ANKS3

ankyrin repeat and sterile alpha motif domain containing 3, the group of Sterile alpha motif domain containing|Ankyrin repeat domain containing

Basic information

Region (hg38): 16:4696510-4734378

Links

ENSG00000168096 ∙ NCBI:124401 ∙ OMIM:617310 ∙ HGNC:29422 ∙ Uniprot:Q6ZW76 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• situs inversus (Supportive), mode of inheritance: AD
• laterality defects, autosomal dominant (Limited), mode of inheritance: AR

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the ANKS3 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ANKS3 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	3	6
missense			60	6	1	67
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region				1		1
non coding						0
Total	0	0	60	9	4

Variants in ANKS3

This is a list of pathogenic ClinVar variants found in the ANKS3 region.

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

Position	Type	Phenotype	Significance	ClinVar
16-4697038-C-CG		Short stature	Pathogenic (Nov 18, 2001)
16-4697072-C-T		not specified	Uncertain significance (Oct 05, 2023)
16-4697341-C-T		not specified	Likely benign (Jan 26, 2022)
16-4697347-C-T		not specified	Uncertain significance (Aug 13, 2021)
16-4697366-A-C		not specified	Uncertain significance (Mar 24, 2023)
16-4697384-T-C		not specified	Uncertain significance (Dec 13, 2021)
16-4697393-G-T		not specified	Uncertain significance (Mar 14, 2023)
16-4697406-G-A			Likely benign (Apr 01, 2022)
16-4697979-G-A		not specified	Uncertain significance (Jun 07, 2024)
16-4697986-G-A		not specified	Uncertain significance (Sep 16, 2021)
16-4697989-C-T		not specified	Uncertain significance (Sep 14, 2023)
16-4697997-C-T		not specified	Uncertain significance (Feb 16, 2023)
16-4698015-G-C		not specified	Uncertain significance (Aug 11, 2024)
16-4698018-G-A		not specified	Uncertain significance (Mar 01, 2023)
16-4698018-G-C		not specified	Uncertain significance (Oct 14, 2023)
16-4698025-C-T		not specified	Uncertain significance (Dec 10, 2024)
16-4698032-C-G			Benign (Jul 04, 2018)
16-4698042-G-A		ANKS3-related disorder	Likely benign (Dec 15, 2022)
16-4698051-G-C		not specified	Uncertain significance (Apr 17, 2023)
16-4698458-G-A		not specified	Uncertain significance (Aug 28, 2024)
16-4698460-G-A		not specified	Uncertain significance (Oct 05, 2023)
16-4698464-G-C		not specified	Uncertain significance (Sep 25, 2023)
16-4698478-C-T		not specified	Likely benign (Apr 08, 2024)
16-4698479-G-A		not specified	Uncertain significance (Oct 20, 2024)
16-4698500-C-T		not specified	Likely benign (Dec 28, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ANKS3	protein_coding	protein_coding	ENST00000304283	15	37867

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.89e-7	0.999	125715	0	33	125748	0.000131

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-1.76	497	398	1.25	0.0000258	4213
Missense in Polyphen		150	159.54	0.94022		1706
Synonymous	-3.89	235	170	1.38	0.0000122	1286
Loss of Function	2.83	17	35.1	0.484	0.00000184	384

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000208	0.000208
Ashkenazi Jewish	0.000614	0.000595
East Asian	0.000123	0.000109
Finnish	0.000237	0.000231
European (Non-Finnish)	0.0000893	0.0000879
Middle Eastern	0.000123	0.000109
South Asian	0.0000980	0.0000980
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Recessive Scores

• pRec: 0.0991

Intolerance Scores

• loftool: 0.617
• rvis_EVS: 0.01
• rvis_percentile_EVS: 54.16

Haploinsufficiency Scores

• pHI: 0.0625
• hipred: N
• hipred_score: 0.492
• ghis: 0.534

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.133

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Anks3

Zebrafish Information Network

• Gene name: anks3
• Affected structure: pronephric tubule
• Phenotype tag: abnormal
• Phenotype quality: cystic

Gene ontology

• Molecular function: protein binding