BTF3L4

basic transcription factor 3 like 4

Basic information

Region (hg38): 1:52056199-52090716

Links

ENSG00000134717 ∙ NCBI:91408 ∙ ∙ HGNC:30547 ∙ Uniprot:Q96K17 ∙ 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 BTF3L4 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the BTF3L4 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			8			8
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	8	0	0

Variants in BTF3L4

This is a list of pathogenic ClinVar variants found in the BTF3L4 region.

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

Position	Type	Phenotype	Significance	ClinVar
1-52059866-G-A		not specified	Uncertain significance (Nov 15, 2021)
1-52059884-G-T		not specified	Uncertain significance (Jan 31, 2024)
1-52059887-C-T		not specified	Uncertain significance (Jun 17, 2024)
1-52064889-A-G		not specified	Uncertain significance (Dec 10, 2024)
1-52083371-T-C		not specified	Uncertain significance (Apr 25, 2023)
1-52083428-C-T		not specified	Uncertain significance (Aug 16, 2021)
1-52083535-C-T		not specified	Uncertain significance (May 24, 2023)
1-52083536-G-T		not specified	Uncertain significance (Oct 03, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
BTF3L4	protein_coding	protein_coding	ENST00000313334	5	34592

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.571	0.418	125721	0	3	125724	0.0000119

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.86	35	82.7	0.423	0.00000401	1051
Missense in Polyphen		1	12.062	0.082907		197
Synonymous	1.38	17	26.0	0.655	0.00000111	287
Loss of Function	2.06	1	6.79	0.147	2.85e-7	91

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000291	0.0000291
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.00000882	0.00000879
Middle Eastern	0.00	0.00
South Asian	0.0000327	0.0000327
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Recessive Scores

• pRec: 0.107

Intolerance Scores

• loftool: 0.328
• rvis_EVS: 0.06
• rvis_percentile_EVS: 58

Haploinsufficiency Scores

• pHI: 0.355
• hipred: N
• hipred_score: 0.411
• ghis: 0.675

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.307

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Btf3l4

Gene ontology

• Molecular function: protein binding