IGFL1

protein-coding

IGF like family member 1, the group of IGF like family

Gene summary

The protein encoded by this gene is a member of the insulin-like growth factor family of signaling molecules. The encoded protein is synthesized as a precursor protein and is proteolytically cleaved to form a secreted mature peptide. The mature peptide binds to a receptor, which in mouse was found on the cell surface of T cells. Increased expression of this gene may be linked to psoriasis. [provided by RefSeq, Aug 2016]

MANE transcript

NM_198541.2

Inheritance

—

ClinVar variants

U:25B:1

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 1.46

Max pathogenic AF

—

Genomic locus

chr19:46,229,742-46,231,243

External References & Databases

Ensembl (ENSG00000188293)

Transcript & Mutation Effects

hg38 • Region Span ~1.5 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 IGFL1 variants in ClinVar

1 Conditions Cataloged

not specifiedTotal: 26

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_198541.2. 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						0
missense			25 clinvar	1 clinvar		26
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	25	1	0	26

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 5 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_198541.2	RefSeq	NP_940943.1	4	MANE Select
ENST00000437936.2	Ensembl	ENSP00000415823.1	4	MANE Select
ENST00000864434.1	Ensembl	ENSP00000534493.1	4	Standard
ENST00000864434.2	Ensembl	ENSP00000534493.1	4	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Molecular Function

signaling receptor binding
protein binding

Cellular Component

extracellular space

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000437936
Coding exons: 4
Length: 1492
Individuals with no LoFs: 124625
Homozygous LoFs: 0
Heterozygous LoFs: 30
Defined: 124655
p: 0.000120

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	-0.0536	66	64.8	1.02	0.00000379	718
Missense (PolyPhen)		9	14.787	0.60866		191
Synonymous	0.815	21	26.3	0.798	0.00000179	198
Loss of Function	-1.11	10	6.87	1.46	3.80e-7	71

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00077	0.00071	rare
Latino/Admixed American	0.000087	0.000087	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0.00034	0.00033	rare
Finnish	0	0.0	absent
European (Non-Finnish)	0.000027	0.000027	rare
South Asian	0.00020	0.00020	rare
Other	0.00017	0.00017	rare

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: Probable ligand of the IGFLR1 cell membrane receptor. {ECO:0000269|PubMed:21454693}.;

Recessive Scores

pRec: 0.0936

Intolerance Scores

LoFtool: 0.754
RVIS EVS: 0.68
RVIS percentile EVS: 84.93

Essentials

Essential (CRISPR): N
Essential (CRISPR2): S
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.114

Gene Damage Prediction

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