FASTKD1

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

Basic information

Region (hg38): 2:169528507-169573875

Links

ENSG00000138399 ∙ NCBI:79675 ∙ OMIM:617529 ∙ HGNC:26150 ∙ Uniprot:Q53R41 ∙ 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 FASTKD1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the FASTKD1 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			46	3		49
nonsense					1	1
start loss						0
frameshift					1	1
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	46	3	2

Variants in FASTKD1

This is a list of pathogenic ClinVar variants found in the FASTKD1 region.

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

Position	Type	Phenotype	Significance	ClinVar
2-169529836-A-G		not specified	Uncertain significance (Sep 14, 2023)
2-169529875-T-C		not specified	Uncertain significance (Dec 16, 2022)
2-169530588-T-C		not specified	Uncertain significance (Jul 06, 2021)
2-169530622-G-GT			Benign (Jan 19, 2018)
2-169530687-A-C		not specified	Uncertain significance (Apr 25, 2022)
2-169531354-T-G		not specified	Uncertain significance (Jan 23, 2024)
2-169531376-G-C			Benign (Jun 26, 2018)
2-169531430-G-A		not specified	Uncertain significance (Aug 02, 2022)
2-169531439-T-C		not specified	Uncertain significance (Mar 27, 2023)
2-169531449-A-T		Glaucoma 1, open angle, B	Pathogenic (Jul 20, 2017)
2-169531451-G-A		not specified	Uncertain significance (Jun 04, 2024)
2-169537247-G-A		not specified	Uncertain significance (Jan 27, 2022)
2-169537319-G-A		not specified	Uncertain significance (May 31, 2022)
2-169537326-C-T		not specified	Likely benign (Jan 26, 2023)
2-169538036-C-T		not specified	Uncertain significance (May 23, 2023)
2-169538129-G-A		not specified	Uncertain significance (Oct 20, 2021)
2-169544746-G-C		not specified	Uncertain significance (Aug 17, 2021)
2-169544807-A-G		not specified	Uncertain significance (Feb 16, 2023)
2-169546329-A-T		not specified	Likely benign (May 27, 2022)
2-169546355-C-T		not specified	Uncertain significance (Oct 13, 2023)
2-169546417-C-T		not specified	Uncertain significance (Apr 20, 2023)
2-169546442-G-A		not specified	Uncertain significance (Jan 23, 2024)
2-169546494-T-A		not specified	Uncertain significance (Mar 18, 2024)
2-169546606-C-T		not specified	Uncertain significance (Nov 21, 2023)
2-169546649-A-G		not specified	Uncertain significance (Feb 06, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
FASTKD1	protein_coding	protein_coding	ENST00000453153	14	44127

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
4.56e-29	0.0000358	123687	17	2043	125747	0.00822

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.553	400	432	0.925	0.0000219	5588
Missense in 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

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00428	0.00427
Ashkenazi Jewish	0.00454	0.00447
East Asian	0.000672	0.000653
Finnish	0.0143	0.0142
European (Non-Finnish)	0.0128	0.0126
Middle Eastern	0.000672	0.000653
South Asian	0.00424	0.00396
Other	0.00798	0.00768

dbNSFP

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

Haploinsufficiency Scores

• pHI: 0.212
• hipred: N
• hipred_score: 0.144
• ghis: 0.519

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.394

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Fastkd1

Gene ontology

• Biological process: mitochondrial RNA metabolic process;protein phosphorylation;regulation of mitochondrial mRNA stability;cellular respiration
• Cellular component: mitochondrion
• Molecular function: RNA binding;protein kinase activity