FASTKD3

FAST kinase domains 3, the group of FASTK mitochondrial RNA binding family

Basic information

Region (hg38): 5:7859158-7869037

Links

ENSG00000124279 ∙ NCBI:79072 ∙ OMIM:617530 ∙ HGNC:28758 ∙ Uniprot:Q14CZ7 ∙ 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 FASTKD3 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the FASTKD3 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					1	1
missense			25	8	1	34
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	25	8	2

Variants in FASTKD3

This is a list of pathogenic ClinVar variants found in the FASTKD3 region.

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

Position	Type	Phenotype	Significance	ClinVar
5-7859468-A-T		not specified	Uncertain significance (Apr 13, 2022)
5-7862876-C-T		not specified	Uncertain significance (May 14, 2024)
5-7862942-G-A		not specified	Uncertain significance (Aug 17, 2022)
5-7862966-T-G		not specified	Uncertain significance (Jan 22, 2024)
5-7865953-C-T		not specified	Uncertain significance (Jun 10, 2022)
5-7865956-C-A		not specified	Uncertain significance (Jan 27, 2022)
5-7866654-C-T		not specified	Likely benign (Jul 30, 2023)
5-7866676-A-G		not specified	Uncertain significance (Jan 30, 2024)
5-7866709-C-G			Benign (Jun 05, 2018)
5-7866788-C-A			Benign (Jun 05, 2018)
5-7866817-G-A		not specified	Uncertain significance (Nov 08, 2022)
5-7866828-T-C		not specified	Uncertain significance (Jun 24, 2022)
5-7866871-G-A		not specified	Uncertain significance (Nov 21, 2022)
5-7866922-T-C		not specified	Uncertain significance (Nov 22, 2021)
5-7866934-G-A		not specified	Uncertain significance (Jun 23, 2023)
5-7866960-A-G		not specified	Uncertain significance (Apr 12, 2024)
5-7866981-G-A		not specified	Uncertain significance (Dec 18, 2023)
5-7867058-T-C		not specified	Likely benign (Jan 18, 2023)
5-7867065-G-A		not specified	Uncertain significance (Dec 19, 2022)
5-7867086-T-C		not specified	Uncertain significance (Sep 19, 2022)
5-7867095-G-C		not specified	Uncertain significance (Mar 07, 2023)
5-7867225-T-C		not specified	Likely benign (Mar 23, 2022)
5-7867295-C-G		not specified	Uncertain significance (Jun 17, 2022)
5-7867296-A-C		not specified	Uncertain significance (Mar 19, 2024)
5-7867340-C-A		not specified	Uncertain significance (Jan 08, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
FASTKD3	protein_coding	protein_coding	ENST00000264669	6	9879

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
5.86e-10	0.402	125625	0	122	125747	0.000485

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.814	296	338	0.875	0.0000171	4323
Missense in Polyphen		68	83.074	0.81855		1138
Synonymous	-0.119	134	132	1.01	0.00000679	1289
Loss of Function	1.01	17	22.1	0.769	0.00000110	320

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00158	0.00157
Ashkenazi Jewish	0.00	0.00
East Asian	0.000381	0.000381
Finnish	0.00	0.00
European (Non-Finnish)	0.000623	0.000571
Middle Eastern	0.000381	0.000381
South Asian	0.000361	0.000359
Other	0.000326	0.000326

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Required for normal mitochondrial respiration (PubMed:20869947). Increases steady-state levels and half-lives of a subset of mature mitochondrial mRNAs MT-ND2, MT-ND3, MT-CYTB, MT-CO2, and MT-ATP8/6. Promotes MT-CO1 mRNA translation and increases mitochondrial complex IV assembly and activity (PubMed:27789713). {ECO:0000269|PubMed:20869947, ECO:0000269|PubMed:27789713}.

Recessive Scores

• pRec: 0.0618

Intolerance Scores

• loftool: 0.903
• rvis_EVS: 0.29
• rvis_percentile_EVS: 71.57

Haploinsufficiency Scores

• pHI: 0.0366
• hipred: N
• hipred_score: 0.144
• ghis: 0.499

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.140

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Fastkd3

Gene ontology

• Biological process: protein phosphorylation;mitochondrial respiratory chain complex IV assembly;regulation of mitochondrial mRNA stability;cellular respiration;positive regulation of mitochondrial translation
• Cellular component: nucleus;mitochondrion
• Molecular function: RNA binding;protein kinase activity;protein binding