KIAA1143

KIAA1143

Basic information

Region (hg38): 3:44737661-44761619

Links

ENSG00000163807 ∙ NCBI:57456 ∙ ∙ HGNC:29198 ∙ Uniprot:Q96AT1 ∙ 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 KIAA1143 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the KIAA1143 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			15			15
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	15	0	0

Variants in KIAA1143

This is a list of pathogenic ClinVar variants found in the KIAA1143 region.

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

Position	Type	Phenotype	Significance	ClinVar
3-44753363-T-A		not specified	Uncertain significance (Jan 31, 2023)
3-44753378-C-T		not specified	Uncertain significance (Jun 11, 2021)
3-44753399-T-C		not specified	Uncertain significance (Oct 04, 2024)
3-44753415-C-G		not specified	Uncertain significance (May 23, 2023)
3-44753435-T-C		not specified	Uncertain significance (Aug 12, 2021)
3-44753486-T-C		not specified	Uncertain significance (Feb 01, 2023)
3-44753513-C-T		not specified	Uncertain significance (Sep 16, 2021)
3-44754227-C-T		not specified	Uncertain significance (Apr 07, 2022)
3-44754284-C-T		not specified	Uncertain significance (Mar 03, 2025)
3-44754346-T-C		not specified	Uncertain significance (Sep 22, 2022)
3-44761512-G-T		not specified	Uncertain significance (Aug 12, 2021)
3-44761541-A-C		not specified	Uncertain significance (Dec 03, 2024)
3-44761559-G-C		not specified	Uncertain significance (Oct 11, 2024)
3-44761584-C-T		not specified	Uncertain significance (Mar 06, 2023)
3-44761589-T-C		not specified	Uncertain significance (Oct 07, 2024)
3-44761597-G-C		not specified	Uncertain significance (May 05, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
KIAA1143	protein_coding	protein_coding	ENST00000296121	3	24002

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00796	0.800	125715	0	31	125746	0.000123

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.0379	83	82.0	1.01	0.00000382	1006
Missense in Polyphen		27	18.349	1.4715		229
Synonymous	-1.76	45	32.3	1.39	0.00000171	280
Loss of Function	1.01	4	6.86	0.583	3.54e-7	93

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000352	0.000351
Ashkenazi Jewish	0.00	0.00
East Asian	0.000109	0.000109
Finnish	0.00	0.00
European (Non-Finnish)	0.0000441	0.0000439
Middle Eastern	0.000109	0.000109
South Asian	0.000396	0.000392
Other	0.000163	0.000163

dbNSFP

Source: dbNSFP

Intolerance Scores

• loftool: 0.645
• rvis_EVS: 0.53
• rvis_percentile_EVS: 80.58

Haploinsufficiency Scores

• pHI: 0.258
• hipred: N
• hipred_score: 0.250
• ghis: 0.453

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.700

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: 1110059G10Rik
• Phenotype: homeostasis/metabolism phenotype; skeleton phenotype

Gene ontology

• Molecular function: protein binding