FDXACB1

protein-coding

ferredoxin-fold anticodon binding domain containing 1

Gene summary

This gene encodes a protein which contains a ferredoxin-fold anticodon-binding domain which is contained in a subset of phenylalanyl tRNA synthetases. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Aug 2011]

MANE transcript

NM_138378.3

Inheritance

—

ClinVar variants

U:93B:10

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.78

Max pathogenic AF

—

Genomic locus

chr11:111,874,056-111,881,243

External References & Databases

Ensembl (ENSG00000255561)

Transcript & Mutation Effects

hg38 • Region Span ~7.2 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 FDXACB1 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 92

not providedTotal: 2

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_138378.3. 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	2 clinvar		3
missense			89 clinvar	8 clinvar		97
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			3 clinvar			3
Total	0	0	93	10	0	103

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 11 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_138378.3	RefSeq	NP_612387.1	5	MANE Select
ENST00000260257.9	Ensembl	ENSP00000260257.4	5	MANE Select
ENST00000528274.2	Ensembl	ENSP00000435572.1	4	Standard
ENST00000531487.1	Ensembl	ENSP00000431629.1	2	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

rRNA base methylation

Molecular Function

protein binding
rRNA (uridine-N3-)-methyltransferase activity

Cellular Component

cytoplasm

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000260257
Coding exons: 5
Length: 7188
Individuals with no LoFs: 124384
Homozygous LoFs: 0
Heterozygous LoFs: 254
Defined: 124638
p: 0.00102

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.0741	316	320	0.988	0.0000151	4095
Missense (PolyPhen)		91	102.78	0.88537		1364
Synonymous	-0.927	138	125	1.11	0.00000622	1217
Loss of Function	0.935	17	21.7	0.783	0.00000101	274

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00026	0.00026	rare
Latino/Admixed American	0.0054	0.0047	notable
Ashkenazi Jewish	0.00030	0.00030	rare
East Asian	0.00045	0.00045	rare
Finnish	0	0.0	absent
European (Non-Finnish)	0.00035	0.00033	rare
South Asian	0.0012	0.0012	notable
Other	0.00036	0.00033	rare

dbNSFP Gene Annotations

Source: dbNSFP

Intolerance Scores

LoFtool: 0.900
RVIS EVS: 0.43
RVIS percentile EVS: 77.29

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.282

Gene Damage Prediction

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