ANKRD28

ankyrin repeat domain 28, the group of Cilia and flagella associated|Ankyrin repeat domain containing|MicroRNA protein coding host genes|Protein phosphatase 1 regulatory subunits|Protein phosphatase 6 regulatory subunits

Basic information

Region (hg38): 3:15667236-15859771

Links

ENSG00000206560 ∙ NCBI:23243 ∙ OMIM:611122 ∙ HGNC:29024 ∙ Uniprot:O15084 ∙ 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 ANKRD28 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ANKRD28 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
missense			77			77
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding				2		2
Total	0	0	77	7	0

Variants in ANKRD28

This is a list of pathogenic ClinVar variants found in the ANKRD28 region.

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

Position	Type	Phenotype	Significance	ClinVar
3-15668073-G-A			Likely benign (Sep 01, 2022)
3-15670283-G-C		not specified	Uncertain significance (Nov 09, 2023)
3-15670341-T-A		not specified	Uncertain significance (Feb 16, 2023)
3-15670346-T-C		not specified	Uncertain significance (May 14, 2024)
3-15670382-A-G		not specified	Uncertain significance (Dec 16, 2024)
3-15670388-A-G		not specified	Uncertain significance (Apr 05, 2023)
3-15670407-T-C		not specified	Uncertain significance (Oct 20, 2024)
3-15670427-C-T		not specified	Uncertain significance (Oct 16, 2024)
3-15670463-C-G		not specified	Uncertain significance (Aug 21, 2024)
3-15670552-A-G			Likely benign (Sep 01, 2024)
3-15676984-C-A		not specified	Uncertain significance (Feb 06, 2024)
3-15676987-C-T		not specified	Uncertain significance (Aug 30, 2022)
3-15677010-C-T		not specified	Uncertain significance (Apr 25, 2022)
3-15677513-A-T		not specified	Uncertain significance (Oct 13, 2023)
3-15677540-A-C		not specified	Uncertain significance (Oct 14, 2023)
3-15678257-T-C		not specified	Uncertain significance (Nov 20, 2024)
3-15678277-T-C		not specified	Uncertain significance (Dec 15, 2023)
3-15678283-T-G		not specified	Uncertain significance (Oct 16, 2023)
3-15678311-A-G			Likely benign (Nov 01, 2023)
3-15678315-C-T			Likely benign (Oct 01, 2024)
3-15679305-C-T		not specified	Uncertain significance (Dec 17, 2023)
3-15679314-C-T		not specified	Uncertain significance (Dec 06, 2023)
3-15679373-T-C		not specified	Uncertain significance (Jan 30, 2024)
3-15679506-C-T		not specified	Uncertain significance (Feb 15, 2023)
3-15679549-C-T		not specified	Uncertain significance (Mar 15, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ANKRD28	protein_coding	protein_coding	ENST00000399451	28	192536

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.00	0.00000265	124626	0	10	124636	0.0000401

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.39	390	547	0.713	0.0000271	6833
Missense in Polyphen		117	207.22	0.56462		2583
Synonymous	1.28	178	201	0.885	0.0000107	2024
Loss of Function	6.27	4	53.5	0.0747	0.00000280	697

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000646	0.0000646
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.000191	0.000186
European (Non-Finnish)	0.0000444	0.0000442
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Putative regulatory subunit of protein phosphatase 6 (PP6) that may be involved in the recognition of phosphoprotein substrates. Involved in the PP6-mediated dephosphorylation of NFKBIE opposing its degradation in response to TNF-alpha. Selectively inhibits the phosphatase activity of PPP1C. Targets PPP1C to modulate HNRPK phosphorylation. {ECO:0000269|PubMed:16564677, ECO:0000269|PubMed:18186651}.
• Pathway: Vesicle-mediated transport;Membrane Trafficking;Post-translational protein modification;Metabolism of proteins;Transport to the Golgi and subsequent modification;Asparagine N-linked glycosylation;COPII-mediated vesicle transport;ER to Golgi Anterograde Transport (Consensus)

Recessive Scores

• pRec: 0.0968

Intolerance Scores

• rvis_EVS: -0.8
• rvis_percentile_EVS: 12.49

Haploinsufficiency Scores

• pHI: 0.352
• hipred: Y
• hipred_score: 0.699
• ghis: 0.555

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.708

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Ankrd28

Gene ontology

• Biological process: COPII vesicle coating
• Cellular component: Golgi membrane;nucleoplasm;cytosol
• Molecular function: protein binding