FYTTD1

forty-two-three domain containing 1, the group of Transcription and export complex 1 subunits

Basic information

Region (hg38): 3:197737179-197787596

Links

ENSG00000122068 ∙ NCBI:84248 ∙ OMIM:616933 ∙ HGNC:25407 ∙ Uniprot:Q96QD9 ∙ 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 FYTTD1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the FYTTD1 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				1		1
missense			25			25
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	25	1	0

Variants in FYTTD1

This is a list of pathogenic ClinVar variants found in the FYTTD1 region.

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

Position	Type	Phenotype	Significance	ClinVar
3-197749997-T-C		not specified	Uncertain significance (Oct 19, 2024)
3-197750027-C-G		not specified	Uncertain significance (Jun 21, 2023)
3-197750033-C-A		not specified	Uncertain significance (Jan 10, 2023)
3-197756452-G-A		not specified	Uncertain significance (Dec 19, 2022)
3-197756497-C-G		not specified	Uncertain significance (Feb 08, 2025)
3-197756536-T-C		not specified	Uncertain significance (Jan 31, 2024)
3-197756538-G-C		not specified	Uncertain significance (Feb 05, 2024)
3-197768486-A-G		not specified	Uncertain significance (Dec 16, 2024)
3-197768500-T-G		not specified	Uncertain significance (Jan 25, 2023)
3-197768532-C-T		not specified	Uncertain significance (Dec 09, 2024)
3-197768533-G-A		not specified	Likely benign (Nov 25, 2024)
3-197768552-A-G		not specified	Uncertain significance (Nov 26, 2024)
3-197770168-G-A		not specified	Uncertain significance (Sep 11, 2024)
3-197770211-C-T		not specified	Uncertain significance (Nov 09, 2024)
3-197773449-C-A		not specified	Uncertain significance (Jul 17, 2024)
3-197773479-C-T		not specified	Uncertain significance (Oct 01, 2024)
3-197773489-G-A		not specified	Uncertain significance (Dec 26, 2023)
3-197774185-G-A		not specified	Uncertain significance (Jul 27, 2024)
3-197774195-C-G		not specified	Uncertain significance (Jul 08, 2022)
3-197776932-G-A		not specified	Uncertain significance (Oct 24, 2024)
3-197776957-T-G		not specified	Uncertain significance (Aug 02, 2021)
3-197776995-G-A		not specified	Uncertain significance (Mar 19, 2024)
3-197776997-C-T		not specified	Uncertain significance (May 31, 2023)
3-197778348-C-A		not specified	Uncertain significance (Oct 29, 2024)
3-197778360-C-T		not specified	Uncertain significance (Jun 11, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
FYTTD1	protein_coding	protein_coding	ENST00000241502	9	50418

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.395	0.605	125741	0	6	125747	0.0000239

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.608	152	175	0.870	0.00000974	2049
Missense in Polyphen		52	72.42	0.71803		794
Synonymous	0.855	53	61.5	0.861	0.00000317	628
Loss of Function	3.06	4	18.1	0.222	0.00000108	202

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000592	0.0000592
Ashkenazi Jewish	0.0000995	0.0000992
East Asian	0.0000544	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.0000105	0.00000879
Middle Eastern	0.0000544	0.0000544
South Asian	0.00	0.00
Other	0.000168	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Required for mRNA export from the nucleus to the cytoplasm. Acts as an adapter that uses the DDX39B/UAP56-NFX1 pathway to ensure efficient mRNA export and delivering to the nuclear pore. Associates with spliced and unspliced mRNAs simultaneously with ALYREF/THOC4. {ECO:0000269|PubMed:19836239}.
• Pathway: Gene expression (Transcription);RNA Polymerase II Transcription;Metabolism of RNA;Cleavage of Growing Transcript in the Termination Region ;RNA Polymerase II Transcription Termination;Transport of Mature mRNA derived from an Intron-Containing Transcript;mRNA 3,-end processing;Transport of Mature Transcript to Cytoplasm;Processing of Capped Intron-Containing Pre-mRNA (Consensus)

Recessive Scores

• pRec: 0.104

Intolerance Scores

• loftool: 0.465
• rvis_EVS: 0.04
• rvis_percentile_EVS: 56.92

Haploinsufficiency Scores

• pHI: 0.158
• hipred: Y
• hipred_score: 0.530
• ghis: 0.599

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.281

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Fyttd1

Gene ontology

• Biological process: mRNA export from nucleus
• Cellular component: nucleoplasm;nuclear speck
• Molecular function: RNA binding;mRNA binding;protein binding