IFT25

intraflagellar transport 25, the group of Small heat shock proteins|IFT-B1 complex

Basic information

Region (hg38): 1:53916574-53945699

Previous symbols: [ "C1orf41", "HSPB11" ]

Links

ENSG00000081870 ∙ NCBI:51668 ∙ ∙ HGNC:25019 ∙ Uniprot:Q9Y547 ∙ 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 IFT25 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the IFT25 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			11			11
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding					8	8
Total	0	0	11	0	8

Variants in IFT25

This is a list of pathogenic ClinVar variants found in the IFT25 region.

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

Position	Type	Phenotype	Significance	ClinVar
1-53921661-A-G		not specified	Uncertain significance (Jun 02, 2024)
1-53921722-C-T		not specified	Uncertain significance (Feb 22, 2023)
1-53921752-C-T		not specified	Uncertain significance (Dec 01, 2023)
1-53921904-T-C			Benign (May 12, 2021)
1-53923798-C-A			Benign (May 12, 2021)
1-53923844-G-GT			Benign (May 12, 2021)
1-53923985-T-G			Benign (May 12, 2021)
1-53924101-TAG-T			Benign (May 12, 2021)
1-53928374-T-G		not specified	Uncertain significance (Sep 26, 2024)
1-53928413-G-A		not specified	Uncertain significance (Feb 08, 2025)
1-53928416-C-T		not specified	Uncertain significance (Jun 28, 2024)
1-53928480-T-C			Benign (May 21, 2021)
1-53929815-G-C			Benign (May 12, 2021)
1-53930000-CA-C			Benign (May 12, 2021)
1-53930041-A-T		not specified	Uncertain significance (Aug 01, 2024)
1-53930049-T-G		not specified	Uncertain significance (Nov 28, 2023)
1-53930060-G-GC		Renal agenesis	Uncertain significance (Apr 29, 2021)
1-53930077-T-C		not specified	Uncertain significance (Jun 17, 2024)
1-53939991-A-G		not specified	Uncertain significance (Feb 15, 2023)
1-53940043-C-T		not specified	Uncertain significance (Jul 14, 2021)
1-53940072-A-G		not specified	Uncertain significance (Jun 22, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
IFT25	protein_coding	protein_coding	ENST00000194214	5	29356

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00202	0.756	124756	0	16	124772	0.0000641

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.564	61	74.7	0.816	0.00000361	957
Missense in Polyphen		12	28.356	0.4232		383
Synonymous	-0.656	32	27.6	1.16	0.00000164	253
Loss of Function	0.917	5	7.76	0.645	3.27e-7	95

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000927	0.0000927
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000896	0.0000883
Middle Eastern	0.00	0.00
South Asian	0.0000981	0.0000980
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Component of the IFT complex B required for sonic hedgehog/SHH signaling. May mediate transport of SHH components: required for the export of SMO and PTCH1 receptors out of the cilium and the accumulation of GLI2 at the ciliary tip in response to activation of the SHH pathway, suggesting it is involved in the dynamic transport of SHH signaling molecules within the cilium. Not required for ciliary assembly. Its role in intraflagellar transport is mainly seen in tissues rich in ciliated cells such as kidney and testis. Essential for male fertility, spermiogenesis and sperm flagella formation. Plays a role in the early development of the kidney. May be involved in the regulation of ureteric bud initiation (By similarity). {ECO:0000250|UniProtKB:Q9D6H2}.
• Pathway: Intraflagellar transport;Cilium Assembly;Organelle biogenesis and maintenance (Consensus)

Recessive Scores

• pRec: 0.136

Intolerance Scores

• loftool: 0.476
• rvis_EVS: 0.17
• rvis_percentile_EVS: 65.33

Haploinsufficiency Scores

• pHI: 0.120
• hipred: N
• hipred_score: 0.284
• ghis: 0.588

Essentials

• essential_gene_CRISPR: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.539

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Hspb11
• Phenotype: respiratory system phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); embryo phenotype; cardiovascular system phenotype (the observable morphological and physiological characteristics of the mammalian heart, blood vessels, or circulatory system that are manifested through development and lifespan); mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); digestive/alimentary phenotype; nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan); limbs/digits/tail phenotype; skeleton phenotype; homeostasis/metabolism phenotype; growth/size/body region phenotype; craniofacial phenotype

Gene ontology

• Biological process: skeletal system development;kidney development;smoothened signaling pathway;spermatogenesis;heart development;cell differentiation;lung development;intraciliary transport involved in cilium assembly;cilium assembly;left/right axis specification
• Cellular component: centrosome;cilium;intraciliary transport particle B;ciliary tip
• Molecular function: protein binding;metal ion binding