FASTKD5

FAST kinase domains 5, the group of FASTK mitochondrial RNA binding family

Basic information

Region (hg38): 20:3146519-3159865

Links

ENSG00000215251 ∙ NCBI:60493 ∙ OMIM:614272 ∙ HGNC:25790 ∙ Uniprot:Q7L8L6 ∙ 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 FASTKD5 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the FASTKD5 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			57	5		62
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	57	5	0

Variants in FASTKD5

This is a list of pathogenic ClinVar variants found in the FASTKD5 region.

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

Position	Type	Phenotype	Significance	ClinVar
20-3146795-A-G		not specified	Uncertain significance (May 26, 2024)
20-3146796-C-T		not specified	Uncertain significance (Jan 27, 2022)
20-3146828-C-A		not specified	Uncertain significance (Dec 12, 2023)
20-3146892-G-A		not specified	Uncertain significance (Jan 03, 2024)
20-3146903-C-T		not specified	Uncertain significance (Jun 07, 2023)
20-3146945-T-C		not specified	Uncertain significance (Dec 13, 2021)
20-3146952-A-G		not specified	Uncertain significance (Sep 11, 2024)
20-3146954-T-C		not specified	Uncertain significance (Aug 28, 2023)
20-3146976-C-A		not specified	Uncertain significance (Dec 17, 2024)
20-3147001-C-T		not specified	Uncertain significance (Jul 31, 2024)
20-3147012-C-T		not specified	Uncertain significance (Oct 10, 2023)
20-3147039-C-T		not specified	Uncertain significance (Dec 10, 2024)
20-3147141-C-A		not specified	Uncertain significance (Apr 06, 2022)
20-3147158-G-C		not specified	Uncertain significance (Apr 18, 2023)
20-3147235-A-C		not specified	Uncertain significance (Jun 19, 2024)
20-3147314-C-T		not specified	Uncertain significance (Jul 25, 2023)
20-3147405-T-G		not specified	Uncertain significance (Dec 17, 2024)
20-3147426-C-T		not specified	Uncertain significance (Nov 27, 2023)
20-3147447-A-G		not specified	Uncertain significance (Jan 08, 2024)
20-3147465-G-A		not specified	Uncertain significance (Apr 15, 2024)
20-3147479-T-C		not specified	Uncertain significance (Jan 19, 2024)
20-3147483-C-G		not specified	Uncertain significance (Nov 06, 2023)
20-3147503-A-T		not specified	Uncertain significance (Dec 30, 2023)
20-3147518-T-C		not specified	Uncertain significance (Oct 26, 2022)
20-3147539-A-G		not specified	Uncertain significance (Dec 28, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
FASTKD5	protein_coding	protein_coding	ENST00000380266	1	13379

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
3.58e-8	0.937	125657	0	91	125748	0.000362

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.557	373	405	0.922	0.0000211	5005
Missense in Polyphen		94	114.2	0.82315		1427
Synonymous	0.0525	155	156	0.995	0.00000783	1528
Loss of Function	1.88	16	26.4	0.605	0.00000171	310

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000485	0.000485
Ashkenazi Jewish	0.000298	0.000298
East Asian	0.000326	0.000326
Finnish	0.000231	0.000231
European (Non-Finnish)	0.000220	0.000220
Middle Eastern	0.000326	0.000326
South Asian	0.00121	0.00121
Other	0.000820	0.000815

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Plays an important role in the processing of non- canonical mitochondrial mRNA precursors (PubMed:25683715). {ECO:0000269|PubMed:25683715}.

Recessive Scores

• pRec: 0.0850

Intolerance Scores

• loftool: 0.761
• rvis_EVS: -0.73
• rvis_percentile_EVS: 14.2

Haploinsufficiency Scores

• pHI: 0.121
• hipred: N
• hipred_score: 0.146
• ghis: 0.495

Essentials

• essential_gene_CRISPR: E
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.990

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Fastkd5
• Phenotype: behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan)

Gene ontology

• Biological process: mitochondrial RNA processing;mRNA processing;protein phosphorylation;cellular respiration
• Cellular component: mitochondrion;ribonucleoprotein granule;mitochondrial nucleoid
• Molecular function: RNA binding;protein kinase activity;protein binding;rRNA binding