IGSF10

protein-coding

immunoglobulin superfamily member 10, the group of MicroRNA protein coding host genes|I-set domain containing

Gene summary

Predicted to be involved in regulation of neuron migration. Predicted to act upstream of or within ossification. Located in extracellular region. [provided by Alliance of Genome Resources, Jul 2025]

MANE transcript

NM_178822.5

Inheritance

AR, AD

ClinVar variants

U:499B:190

Top phenotype

IGSF10-related disorder

gnomAD constraint

pLI —, LoF o/e 1.02

Max pathogenic AF

—

Genomic locus

chr3:151,425,384-151,461,061

External References & Databases

Ensembl (ENSG00000152580)

Transcript & Mutation Effects

hg38 • Region Span ~35.7 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

disorder of sexual differentiationMODERATE

Inheritance Pattern: AR

Disease ID:MONDO:0002145

Submitter: PanelApp Australia

disorder of sexual differentiationMODERATE

Inheritance Pattern: AD

Disease ID:MONDO:0002145

Submitter: PanelApp Australia

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to IGSF10 variants in ClinVar

6 Conditions Cataloged

not specifiedTotal: 402

not providedTotal: 350

IGSF10-related disorderTotal: 71

Premature ovarian failureTotal: 4

EBV-positive nodal T- and NK-cell lymphomaTotal: 1

Martsolf syndrome 1Total: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_178822.5. 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			2 clinvar	68 clinvar	21 clinvar	91
missense			470 clinvar	68 clinvar	22 clinvar	560
nonsense			13 clinvar	4 clinvar		17
start loss						0
frameshift			13 clinvar	6 clinvar	1 clinvar	20
splice donor/acceptor (+/-2bp)			1 clinvar			1
Total	0	0	499	146	44	689

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 22 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_178822.5	RefSeq	NP_849144.2	6	MANE Select
ENST00000282466.4	Ensembl	ENSP00000282466.3	6	MANE Select
NM_001178145.3	RefSeq	NP_001171616.2	1	Standard
NM_001178146.3	RefSeq	NP_001171617.1	1	Standard

Model Organisms & Knockout Phenotypes

Observed phenotypic effects in mouse and zebrafish models

Gene / Model	Organism	Observed Phenotype
igsf10	Danio rerio	Structure: hypothalamus gonadotrophin-releasing hormone neuron development Quality: decreased occurrence abnormal

Gene / Model

Organism

Observed Phenotype

igsf10

Danio rerio

Structure: hypothalamus gonadotrophin-releasing hormone neuron development

Quality: decreased occurrence

abnormal

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

ossification
regulation of neuron migration

Cellular Component

extracellular region

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000282466
Coding exons: 6
Length: 33326
Individuals with no LoFs: 124609
Homozygous LoFs: 1
Heterozygous LoFs: 1138
Defined: 125748
p: 0.00454

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	-1.63	1523	1.35e+3	1.12	0.0000689	17167
Missense (PolyPhen)		458	414.42	1.1052		5298
Synonymous	-1.33	547	509	1.07	0.0000270	5378
Loss of Function	-0.146	73	71.7	1.02	0.00000410	976

Population LoF Frequency

Population	CAF	p-value	Status
African	0.0030	0.0030	notable
Latino/Admixed American	0.0026	0.0025	notable
Ashkenazi Jewish	0.0097	0.0053	notable
East Asian	0.0051	0.0051	notable
Finnish	0.0062	0.0062	notable
European (Non-Finnish)	0.0038	0.0036	notable
South Asian	0.0098	0.0098	notable
Other	0.0034	0.0031	notable

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: Involved in the control of early migration of neurons expressing gonadotropin-releasing hormone (GNRH neurons) (By similarity). May be involved in the maintenance of osteochondroprogenitor cells pool (By similarity). {ECO:0000250|UniProtKB:Q3V1M1, ECO:0000250|UniProtKB:Q6WRH9}.;
Disease: DISEASE: Note=Mutations in IGSF10 may be a cause of self-limited delayed puberty. This common condition is defined as the absence of testicular enlargement in boys or breast development in girls at an age that is 2-2.5 standard deviations later than the population mean. Self-limited delayed puberty segregates within families, with the majority of families displaying an autosomal dominant pattern of inheritance. {ECO:0000269|PubMed:27137492}.;

Recessive Scores

pRec: 0.0926

Intolerance Scores

LoFtool: 0.997
RVIS EVS: 0
RVIS percentile EVS: 54.04

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.449

Gene Damage Prediction

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