FASTKD1

protein-coding

FAST kinase domains 1, the group of FASTK mitochondrial RNA binding family

Gene summary

Enables RNA binding activity. Involved in mitochondrial RNA metabolic process and regulation of mitochondrial mRNA stability. Located in mitochondrion. [provided by Alliance of Genome Resources, Jun 2026]

MANE transcript

NM_024622.6

Inheritance

—

ClinVar variants

P:1U:122B:11

Top phenotype

Glaucoma 1, open angle, B

gnomAD constraint

pLI —, LoF o/e 1.06

Max pathogenic AF

—

Genomic locus

chr2:169,528,508-169,573,875

External References & Databases

Ensembl (ENSG00000138399)

Transcript & Mutation Effects

hg38 • Region Span ~45.4 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to FASTKD1 variants in ClinVar

3 Conditions Cataloged

not specifiedTotal: 120

not providedTotal: 2

Glaucoma 1, open angle, BTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_024622.6. 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			1 clinvar			1
missense	1 clinvar		116 clinvar	9 clinvar		126
nonsense			1 clinvar		1 clinvar	2
start loss						0
frameshift					1 clinvar	1
splice donor/acceptor (+/-2bp)			4 clinvar			4
Total	1	0	122	9	2	134

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 75 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_024622.6	RefSeq	NP_078898.3	14	MANE Select
ENST00000453153.7	Ensembl	ENSP00000400513.2	14	MANE Select
NM_001281476.3	RefSeq	NP_001268405.1	13	Standard
NM_001322046.2	RefSeq	NP_001308975.1	14	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

mitochondrial RNA metabolic process
protein phosphorylation
regulation of mitochondrial mRNA stability
cellular respiration

Molecular Function

RNA binding
protein kinase activity

Cellular Component

mitochondrion

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000453153
Coding exons: 14
Length: 44127
Individuals with no LoFs: 123687
Homozygous LoFs: 17
Heterozygous LoFs: 2043
Defined: 125747
p: 0.00822

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.553	400	432	0.925	0.0000219	5588
Missense (PolyPhen)		85	94.773	0.89688		1426
Synonymous	-0.219	159	156	1.02	0.00000801	1571
Loss of Function	-0.349	42	39.6	1.06	0.00000214	510

Population LoF Frequency

Population	CAF	p-value	Status
African	0.0024	0.0023	notable
Latino/Admixed American	0.0019	0.0019	notable
Ashkenazi Jewish	0.0045	0.0045	notable
East Asian	0.00067	0.00065	rare
Finnish	0.014	0.014	notable
European (Non-Finnish)	0.013	0.013	notable
South Asian	0.0042	0.0040	notable
Other	0.0080	0.0077	notable

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: Regulates the stability of mitochondrial MT-ND3 mRNA (PubMed:28335001). {ECO:0000269|PubMed:28335001}.;

Intolerance Scores

LoFtool: 0.977
RVIS EVS: -0.13
RVIS percentile EVS: 44.05

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.394

Gene Damage Prediction

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