IGFL4

IGF like family member 4, the group of IGF like family

Basic information

Region (hg38): 19:46039181-46077118

Links

ENSG00000204869 ∙ NCBI:444882 ∙ OMIM:610547 ∙ HGNC:32931 ∙ Uniprot:Q6B9Z1 ∙ 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 IGFL4 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the IGFL4 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 IGFL4

This is a list of pathogenic ClinVar variants found in the IGFL4 region.

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

Position	Type	Phenotype	Significance	ClinVar
19-46039920-C-A		not specified	Uncertain significance (Feb 22, 2023)
19-46039930-G-T		not specified	Uncertain significance (Jul 19, 2023)
19-46040180-G-A		not specified	Uncertain significance (Jan 04, 2022)
19-46040216-T-C		not specified	Uncertain significance (Sep 27, 2021)
19-46040300-C-T		not specified	Uncertain significance (Aug 02, 2021)
19-46040309-G-A		not specified	Uncertain significance (May 18, 2023)
19-46040347-C-T		not specified	Uncertain significance (Sep 14, 2021)
19-46040357-A-C		not specified	Uncertain significance (May 31, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
IGFL4	protein_coding	protein_coding	ENST00000377697	4	37371

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00118	0.644	124829	0	5	124834	0.0000200

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.501	54	65.4	0.826	0.00000324	804
Missense in Polyphen		15	18.308	0.8193		247
Synonymous	-0.254	28	26.3	1.06	0.00000151	233
Loss of Function	0.623	5	6.75	0.741	2.89e-7	75

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000580	0.0000580
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.00000890	0.00000890
Middle Eastern	0.00	0.00
South Asian	0.0000654	0.0000654
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Intolerance Scores

• loftool: 0.608
• rvis_EVS: 0.35
• rvis_percentile_EVS: 73.97

Haploinsufficiency Scores

• pHI: 0.111
• hipred: N
• hipred_score: 0.139
• ghis: 0.456

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.114

Gene Damage Prediction

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

Gene ontology

• Cellular component: extracellular space
• Molecular function: signaling receptor binding