KIAA1217

KIAA1217, the group of MicroRNA protein coding host genes

Basic information

Region (hg38): 10:23694745-24547848

Links

ENSG00000120549 ∙ NCBI:56243 ∙ OMIM:617367 ∙ HGNC:25428 ∙ Uniprot:Q5T5P2 ∙ 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 KIAA1217 gene.

• Inborn genetic diseases (77 variants)
• not provided (14 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the KIAA1217 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				4	1	5
missense			72	10	4	86
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	72	14	5

Variants in KIAA1217

This is a list of pathogenic ClinVar variants found in the KIAA1217 region.

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

Position	Type	Phenotype	Significance	ClinVar
10-24209252-G-A		not specified	Uncertain significance (Aug 03, 2022)
10-24219649-G-A		not specified	Uncertain significance (Sep 16, 2021)
10-24219743-T-A		not specified	Uncertain significance (Dec 19, 2023)
10-24219857-A-G		not specified	Uncertain significance (Sep 17, 2021)
10-24219902-G-A		not specified	Uncertain significance (Jan 24, 2024)
10-24380981-C-T		not specified	Uncertain significance (May 25, 2022)
10-24381017-C-T		not specified	Uncertain significance (Nov 15, 2021)
10-24433012-T-C		not specified	Uncertain significance (Aug 23, 2021)
10-24433145-A-G		not specified	Uncertain significance (Oct 17, 2023)
10-24438388-A-G		not specified	Uncertain significance (Mar 29, 2022)
10-24438447-C-T		not specified	Uncertain significance (Mar 04, 2024)
10-24473250-C-A		not specified	Uncertain significance (Jun 11, 2021)
10-24473307-C-T		not specified	Uncertain significance (Apr 25, 2022)
10-24473381-G-A		not specified	Uncertain significance (Jun 29, 2023)
10-24473477-G-A		not specified	Uncertain significance (Sep 22, 2022)
10-24473484-T-C		not specified	Uncertain significance (Nov 17, 2022)
10-24473516-A-T		not specified	Uncertain significance (Sep 07, 2022)
10-24473738-C-G		not specified	Uncertain significance (Jan 06, 2023)
10-24473796-C-G		not specified	Uncertain significance (Sep 20, 2023)
10-24473831-A-G		not specified	Likely benign (Jan 11, 2023)
10-24473861-G-A		not specified	Uncertain significance (Nov 17, 2022)
10-24473888-C-T		not specified	Uncertain significance (Dec 07, 2023)
10-24473931-C-T		not specified	Uncertain significance (Sep 07, 2022)
10-24473955-G-A		not specified	Uncertain significance (Apr 17, 2023)
10-24473960-G-A		not specified	Likely benign (Nov 08, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
KIAA1217	protein_coding	protein_coding	ENST00000376454	21	853098

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.000232	1.00	125678	0	70	125748	0.000278

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.294	1095	1.12e+3	0.975	0.0000650	12757
Missense in Polyphen		554	575.57	0.96252		6691
Synonymous	-1.01	469	442	1.06	0.0000284	3844
Loss of Function	5.55	21	71.8	0.293	0.00000374	908

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000640	0.000639
Ashkenazi Jewish	0.000516	0.000496
East Asian	0.000109	0.000109
Finnish	0.000740	0.000739
European (Non-Finnish)	0.000239	0.000229
Middle Eastern	0.000109	0.000109
South Asian	0.0000980	0.0000980
Other	0.000331	0.000326

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Required for normal development of intervertebral disks. {ECO:0000250|UniProtKB:A2AQ25}.
• Pathway: EGFR1 (Consensus)

Recessive Scores

• pRec: 0.0945

Intolerance Scores

• loftool: 0.533
• rvis_EVS: -3.01
• rvis_percentile_EVS: 0.52

Haploinsufficiency Scores

• pHI: 0.222
• hipred: Y
• hipred_score: 0.604
• ghis: 0.536

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.596

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Etl4
• Phenotype: renal/urinary system phenotype; skeleton phenotype; digestive/alimentary phenotype; limbs/digits/tail phenotype; reproductive system phenotype; 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); normal phenotype; embryo phenotype

Gene ontology

• Biological process: embryonic skeletal system development
• Cellular component: cytoplasm
• Molecular function: molecular_function