IGSF10

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

Basic information

Region (hg38): 3:151425384-151461061

Links

ENSG00000152580 ∙ NCBI:285313 ∙ OMIM:617351 ∙ HGNC:26384 ∙ Uniprot:Q6WRI0 ∙ 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 IGSF10 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the IGSF10 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				52	25	77
missense			216	29	25	270
nonsense			6	2		8
start loss						0
frameshift			10	6	1	17
inframe indel			2	1		3
splice donor/acceptor (+/-2bp)			1			1
splice region				2	1	3
non coding				2	1	3
Total	0	0	235	92	52

Variants in IGSF10

This is a list of pathogenic ClinVar variants found in the IGSF10 region.

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

Position	Type	Phenotype	Significance	ClinVar
3-151430312-G-C		Nizon-Isidor syndrome	Uncertain significance (Nov 19, 2021)
3-151430315-T-G			Uncertain significance (Feb 13, 2023)
3-151430384-A-C			Uncertain significance (Aug 28, 2023)
3-151432756-C-G		Inborn genetic diseases	Uncertain significance (Jan 16, 2024)
3-151432798-C-G		Inborn genetic diseases	Uncertain significance (Aug 02, 2023)
3-151436701-A-C		not specified	Uncertain significance (Sep 13, 2023)
3-151436707-C-T			Likely benign (Sep 07, 2022)
3-151436708-G-A		not specified	Uncertain significance (Nov 06, 2024)
3-151436711-GC-G		Premature ovarian failure	Uncertain significance (Apr 22, 2019)
3-151436721-C-T		IGSF10-related disorder	Benign (Nov 25, 2023)
3-151436724-T-C		not specified	Uncertain significance (Jul 05, 2022)
3-151436748-A-C		not specified	Uncertain significance (Jun 26, 2024)
3-151436807-T-C		not specified	Uncertain significance (Oct 23, 2024)
3-151436826-G-A		IGSF10-related disorder	Benign (Jan 22, 2024)
3-151436831-C-G			Uncertain significance (Jan 15, 2023)
3-151436835-C-G			Uncertain significance (May 26, 2023)
3-151436846-G-A		not specified	Conflicting classifications of pathogenicity (Dec 08, 2023)
3-151436846-G-C		not specified	Uncertain significance (Aug 08, 2022)
3-151436856-G-A		not specified	Uncertain significance (Jul 26, 2024)
3-151436878-T-C		IGSF10-related disorder	Benign (Jan 31, 2024)
3-151436954-C-T		not specified	Uncertain significance (Aug 04, 2023)
3-151436975-C-T			Uncertain significance (Aug 17, 2022)
3-151436990-A-ACAAT			Uncertain significance (Oct 24, 2022)
3-151436993-A-G		IGSF10-related disorder	Benign (Jan 29, 2024)
3-151436996-A-T			Uncertain significance (Aug 11, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
IGSF10	protein_coding	protein_coding	ENST00000282466	6	33326

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
5.80e-49	4.55e-8	124609	1	1138	125748	0.00454

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-1.63	1523	1.35e+3	1.12	0.0000689	17167
Missense in 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

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00552	0.00552
Ashkenazi Jewish	0.00969	0.00527
East Asian	0.00507	0.00507
Finnish	0.00624	0.00621
European (Non-Finnish)	0.00376	0.00358
Middle Eastern	0.00507	0.00507
South Asian	0.00982	0.00978
Other	0.00344	0.00310

dbNSFP

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

Haploinsufficiency Scores

• pHI: 0.198
• hipred: N
• hipred_score: 0.146
• ghis: 0.442

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.449

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Igsf10

Zebrafish Information Network

• Gene name: igsf10
• Affected structure: hypothalamus gonadotrophin-releasing hormone neuron development
• Phenotype tag: abnormal
• Phenotype quality: decreased occurrence

Gene ontology

• Biological process: ossification;regulation of neuron migration
• Cellular component: extracellular region