SCHIP1

schwannomin interacting protein 1, the group of MicroRNA protein coding host genes

Basic information

Region (hg38): 3:159273244-159897629

Links

ENSG00000151967 ∙ NCBI:29970 ∙ OMIM:619206 ∙ HGNC:15678 ∙ Uniprot:P0DPB3 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• complex neurodevelopmental disorder (Limited), mode of inheritance: AR

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the SCHIP1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SCHIP1 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			5			5
nonsense		1				1
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	1	5	0	0

Variants in SCHIP1

This is a list of pathogenic ClinVar variants found in the SCHIP1 region.

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

Position	Type	Phenotype	Significance	ClinVar
3-159764479-G-T		not specified	Uncertain significance (Jun 24, 2022)
3-159764549-A-G		not specified	Uncertain significance (May 26, 2022)
3-159764552-G-C		not specified	Uncertain significance (Nov 22, 2021)
3-159764623-C-T		not specified	Uncertain significance (Jul 26, 2021)
3-159764627-T-G		not specified	Uncertain significance (Dec 20, 2023)
3-159764645-T-C		not specified	Uncertain significance (Jan 08, 2024)
3-159764647-G-A		not specified	Uncertain significance (Apr 07, 2023)
3-159764666-A-T		not specified	Uncertain significance (Dec 04, 2023)
3-159764686-G-A		not specified	Uncertain significance (Dec 20, 2022)
3-159764729-C-T		not specified	Uncertain significance (Apr 23, 2024)
3-159764788-A-G		not specified	Uncertain significance (Jul 09, 2021)
3-159764794-G-T		not specified	Uncertain significance (Mar 25, 2024)
3-159764809-C-T		not specified	Uncertain significance (Jul 05, 2023)
3-159764810-C-T		not specified	Uncertain significance (Jun 29, 2023)
3-159764875-G-A		not specified	Uncertain significance (Nov 17, 2022)
3-159764896-A-G		not specified	Uncertain significance (Jul 06, 2021)
3-159764900-G-C		not specified	Likely benign (Apr 01, 2024)
3-159764914-C-T		not specified	Uncertain significance (May 03, 2023)
3-159764918-G-A		not specified	Uncertain significance (Jul 05, 2023)
3-159764920-G-A		not specified	Uncertain significance (Dec 26, 2023)
3-159764948-G-A		not specified	Uncertain significance (Mar 19, 2024)
3-159765028-C-T		not specified	Uncertain significance (Sep 13, 2023)
3-159765032-C-T		not specified	Uncertain significance (Feb 17, 2022)
3-159765122-G-A		not specified	Uncertain significance (Dec 26, 2023)
3-159866205-C-T		not specified	Uncertain significance (Nov 07, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SCHIP1	protein_coding	protein_coding	ENST00000445224	7	57500

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.987	0.0128	0	0	0	0	0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.90	68	129	0.528	0.00000596	1664
Missense in Polyphen		31	66.379	0.46701		839
Synonymous	0.537	40	44.6	0.898	0.00000233	397
Loss of Function	3.36	0	13.2	0.00	6.95e-7	155

LoF frequencies by population

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

dbNSFP

Source: dbNSFP

• Pathway: Mesodermal Commitment Pathway;Ectoderm Differentiation (Consensus)

Recessive Scores

• pRec: 0.113

Intolerance Scores

• rvis_EVS: -0.1
• rvis_percentile_EVS: 46.49

Haploinsufficiency Scores

• pHI: 0.297
• hipred: N
• hipred_score: 0.372
• ghis: 0.526

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.924

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Low	Low	Low
Primary Immunodeficiency	Low	Low	Low
Cancer	Low	Low	Low

Mouse Genome Informatics

• Gene name: Schip1
• Phenotype: renal/urinary system phenotype; skeleton phenotype; digestive/alimentary phenotype; reproductive system phenotype; 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); 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); cellular phenotype; homeostasis/metabolism phenotype; craniofacial phenotype; muscle phenotype; endocrine/exocrine gland phenotype; growth/size/body region phenotype

Zebrafish Information Network

• Gene name: schip1
• Affected structure: pronephric capsular space
• Phenotype tag: abnormal
• Phenotype quality: dilated

Gene ontology

• Cellular component: cytoplasm
• Molecular function: protein binding;identical protein binding