FASTKD5

protein-coding

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

Gene summary

Enables rRNA binding activity. Involved in mitochondrial RNA processing. Located in mitochondrial nucleoid and ribonucleoprotein granule. [provided by Alliance of Genome Resources, Jul 2025]

MANE transcript

NM_021826.5

Inheritance

ClinVar variants

P:5U:98B:9

Top phenotype

Mitochondrial complex IV deficiency, nuclear type 24

gnomAD constraint

pLI —, LoF o/e 0.61

Max pathogenic AF

—

Genomic locus

chr20:3,146,519-3,159,865

External References & Databases

Ensembl (ENSG00000215251)

Transcript & Mutation Effects

hg38 • Region Span ~13.3 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

Leigh syndromeMODERATE

Inheritance Pattern: AR

Disease ID:MONDO:0009723

Submitter: G2P

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to FASTKD5 variants in ClinVar

4 Conditions Cataloged

not specifiedTotal: 106

Mitochondrial complex IV deficiency, nuclear type 24Total: 5

Leigh syndromeTotal: 5

not providedTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_021826.5. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous						0
missense	3 clinvar		98 clinvar	9 clinvar		110
nonsense						0
start loss						0
frameshift	2 clinvar					2
splice donor/acceptor (+/-2bp)						0
Total	5	0	98	9	0	112

Highest pathogenic variant AF is 0.00006752462

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 10 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_021826.5	RefSeq	NP_068598.1	1	MANE Select
ENST00000380266.4	Ensembl	ENSP00000369618.3	1	MANE Select
ENST00000687419.1	Ensembl	ENSP00000510780.1	1	Standard
ENST00000687419.2	Ensembl	ENSP00000510780.1	1	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

mitochondrial RNA processing
mRNA processing
protein phosphorylation
cellular respiration

Molecular Function

RNA binding
protein kinase activity
protein binding
rRNA binding

Cellular Component

mitochondrion
ribonucleoprotein granule
mitochondrial nucleoid

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000380266
Coding exons: 1
Length: 13379
Individuals with no LoFs: 125657
Homozygous LoFs: 0
Heterozygous LoFs: 91
Defined: 125748
p: 0.000362

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.557	373	405	0.922	0.0000211	5005
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00037	0.00037	rare
Latino/Admixed American	0.00012	0.00012	rare
Ashkenazi Jewish	0.00030	0.00030	rare
East Asian	0.00033	0.00033	rare
Finnish	0.00023	0.00023	rare
European (Non-Finnish)	0.00022	0.00022	rare
South Asian	0.0012	0.0012	notable
Other	0.00082	0.00081	rare

dbNSFP Gene Annotations

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

Essentials

Essential (CRISPR): E
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: E
Indispensability score: 0.990

Gene Damage Prediction

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