ANKRD50

ankyrin repeat domain containing 50, the group of Ankyrin repeat domain containing

Basic information

Region (hg38): 4:124664047-124712732

Links

ENSG00000151458 ∙ NCBI:57182 ∙ OMIM:619856 ∙ HGNC:29223 ∙ Uniprot:Q9ULJ7 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• schizophrenia (No Known Disease Relationship), mode of inheritance: Unknown

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the ANKRD50 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ANKRD50 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
missense			56	1		57
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	56	4	0

Variants in ANKRD50

This is a list of pathogenic ClinVar variants found in the ANKRD50 region.

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

Position	Type	Phenotype	Significance	ClinVar
4-124669129-C-A		not specified	Uncertain significance (Mar 01, 2023)
4-124669156-A-G		not specified	Uncertain significance (Sep 16, 2021)
4-124669177-T-C		not specified	Uncertain significance (Oct 03, 2022)
4-124669219-C-G		not specified	Uncertain significance (Jun 17, 2024)
4-124669304-C-T		not specified	Uncertain significance (May 04, 2023)
4-124669334-T-C		not specified	Uncertain significance (Jun 03, 2022)
4-124669352-G-A		not specified	Uncertain significance (Apr 27, 2023)
4-124669429-C-T		not specified	Uncertain significance (Mar 28, 2022)
4-124669469-C-A		not specified	Uncertain significance (Oct 25, 2023)
4-124669583-T-C		not specified	Uncertain significance (Aug 16, 2021)
4-124669663-G-A		not specified	Uncertain significance (Jun 22, 2024)
4-124669679-T-C		not specified	Uncertain significance (Dec 27, 2023)
4-124669689-T-C			Likely benign (Mar 01, 2023)
4-124669753-T-C		not specified	Uncertain significance (May 09, 2023)
4-124669757-G-A		not specified	Uncertain significance (Jul 07, 2022)
4-124669762-A-C		not specified	Uncertain significance (Aug 02, 2021)
4-124669831-G-A		not specified	Uncertain significance (Mar 15, 2024)
4-124669835-G-A		not specified	Uncertain significance (Jul 31, 2023)
4-124669841-T-A		not specified	Uncertain significance (Mar 14, 2023)
4-124669859-T-C		not specified	Uncertain significance (May 17, 2023)
4-124669943-G-C		not specified	Uncertain significance (Jun 13, 2023)
4-124669951-G-C		not specified	Uncertain significance (Dec 20, 2023)
4-124670168-C-T		not specified	Likely benign (Jun 23, 2023)
4-124670174-C-G		not specified	Uncertain significance (Feb 12, 2024)
4-124670317-C-G		not specified	Uncertain significance (Sep 17, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ANKRD50	protein_coding	protein_coding	ENST00000504087	3	48681

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.979	0.0208	125701	0	46	125747	0.000183

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.705	683	737	0.927	0.0000383	9295
Missense in Polyphen		176	241.86	0.72769		2982
Synonymous	-1.06	298	276	1.08	0.0000145	2876
Loss of Function	5.49	9	51.5	0.175	0.00000309	647

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000699	0.000699
Ashkenazi Jewish	0.0000996	0.0000992
East Asian	0.000163	0.000163
Finnish	0.0000462	0.0000462
European (Non-Finnish)	0.000106	0.000105
Middle Eastern	0.000163	0.000163
South Asian	0.0000983	0.0000980
Other	0.000330	0.000326

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Involved in the endosome-to-plasma membrane trafficking and recycling of SNX27-retromer-dependent cargo proteins, such as GLUT1 (PubMed:25278552).

Recessive Scores

• pRec: 0.109

Intolerance Scores

• loftool: 0.493
• rvis_EVS: -1.74
• rvis_percentile_EVS: 2.39

Haploinsufficiency Scores

• pHI: 0.0848
• hipred: N
• hipred_score: 0.427
• ghis: 0.599

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.310

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Ankrd50

Gene ontology

• Biological process: protein transport;retrograde transport, endosome to plasma membrane
• Cellular component: endosome
• Molecular function: protein binding