ANKRD13D

ankyrin repeat domain 13D, the group of Ankyrin repeat domain containing

Basic information

Region (hg38): 11:67289300-67302485

Links

ENSG00000172932 ∙ NCBI:338692 ∙ OMIM:615126 ∙ HGNC:27880 ∙ Uniprot:Q6ZTN6 ∙ 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 ANKRD13D gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ANKRD13D 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						0
missense			33			33
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	33	0	0

Variants in ANKRD13D

This is a list of pathogenic ClinVar variants found in the ANKRD13D region.

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

Position	Type	Phenotype	Significance	ClinVar
11-67289483-T-G		not specified	Uncertain significance (Jul 25, 2023)
11-67289492-A-C		not specified	Uncertain significance (Feb 14, 2024)
11-67289497-C-G		not specified	Uncertain significance (Feb 14, 2024)
11-67289512-C-T		not specified	Uncertain significance (Feb 27, 2024)
11-67290103-G-A		not specified	Uncertain significance (Nov 13, 2023)
11-67290204-G-A		not specified	Uncertain significance (Dec 06, 2021)
11-67290346-G-T			Uncertain significance (-)
11-67291653-C-T		not specified	Uncertain significance (Nov 08, 2022)
11-67291695-G-A		not specified	Uncertain significance (Mar 28, 2024)
11-67291714-G-A		not specified	Uncertain significance (Feb 10, 2022)
11-67291720-G-A		not specified	Uncertain significance (Feb 03, 2022)
11-67292027-G-A		not specified	Uncertain significance (Aug 04, 2023)
11-67292059-A-C		not specified	Uncertain significance (Mar 16, 2022)
11-67292093-T-C		not specified	Uncertain significance (Nov 01, 2022)
11-67292117-C-T		not specified	Uncertain significance (May 16, 2024)
11-67292119-A-C		not specified	Uncertain significance (Dec 13, 2021)
11-67292137-A-G		not specified	Uncertain significance (Jan 31, 2024)
11-67299094-G-T		not specified	Uncertain significance (Sep 26, 2023)
11-67299116-G-A		not specified	Uncertain significance (Jan 08, 2024)
11-67299537-G-A		not specified	Uncertain significance (Jan 03, 2022)
11-67299573-C-T		not specified	Uncertain significance (Apr 01, 2024)
11-67299886-G-A		not specified	Uncertain significance (Oct 03, 2023)
11-67300093-G-T		not specified	Uncertain significance (Nov 14, 2023)
11-67301094-A-G		not specified	Uncertain significance (Jan 09, 2024)
11-67301109-T-C		not specified	Uncertain significance (Mar 28, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ANKRD13D	protein_coding	protein_coding	ENST00000511455	15	13939

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.349	0.651	125719	0	21	125740	0.0000835

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.64	296	387	0.765	0.0000250	3883
Missense in Polyphen		101	155.85	0.64805		1550
Synonymous	1.13	143	161	0.887	0.0000108	1236
Loss of Function	3.97	7	30.8	0.228	0.00000145	326

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000240	0.000239
Ashkenazi Jewish	0.00	0.00
East Asian	0.000109	0.000109
Finnish	0.0000929	0.0000924
European (Non-Finnish)	0.0000766	0.0000703
Middle Eastern	0.000109	0.000109
South Asian	0.0000327	0.0000327
Other	0.000327	0.000326

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Ubiquitin-binding protein that specifically recognizes and binds 'Lys-63'-linked ubiquitin. Does not bind 'Lys-48'-linked ubiquitin. Positively regulates the internalization of ligand- activated EGFR by binding to the Ub moiety of ubiquitinated EGFR at the cell membrane. {ECO:0000269|PubMed:22298428}.

Recessive Scores

• pRec: 0.104

Intolerance Scores

• loftool: 0.318
• rvis_EVS: -0.98
• rvis_percentile_EVS: 8.8

Haploinsufficiency Scores

• pHI: 0.123
• hipred: Y
• hipred_score: 0.572
• ghis: 0.631

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.340

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Ankrd13d
• Phenotype: skeleton phenotype

Gene ontology

• Cellular component: late endosome;plasma membrane