SCHIP1

protein-coding

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

Gene summary

Enables identical protein binding activity. Predicted to be involved in positive regulation of hippo signaling. Predicted to act upstream of or within several processes, including face morphogenesis; fibroblast migration; and luteinization. Located in cytosol. [provided by Alliance of Genome Resources, Jun 2026]

MANE transcript

NM_014575.4

Inheritance

ClinVar variants

P:1U:67B:1

Top phenotype

Familial meningioma

gnomAD constraint

pLI —, LoF o/e 0

Max pathogenic AF

—

Genomic locus

chr3:159,273,244-159,897,629

External References & Databases

Ensembl (ENSG00000151967)

Transcript & Mutation Effects

hg38 • Region Span ~624.4 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

complex neurodevelopmental disorderLIMITED

Inheritance Pattern: AR

Disease ID:MONDO:0100038

Submitter: Ambry Genetics

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to SCHIP1 variants in ClinVar

3 Conditions Cataloged

not specifiedTotal: 66

not providedTotal: 2

Familial meningiomaTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_014575.4. 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			67 clinvar	1 clinvar		68
nonsense		1 clinvar				1
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	1	67	1	0	69

Highest pathogenic variant AF is 0.0000018588236

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 47 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_014575.4	RefSeq	NP_055390.1	8	MANE Select
ENST00000638749.2	Ensembl	ENSP00000491030.1	8	MANE Select
NM_001197107.2	RefSeq	NP_001184036.1	8	Standard
NM_001197108.2	RefSeq	NP_001184037.1	7	Standard

Model Organisms & Knockout Phenotypes

Observed phenotypic effects in mouse and zebrafish models

Gene / Model	Organism	Observed Phenotype
schip1	Danio rerio	Structure: pronephric capsular space Quality: dilated abnormal

Gene / Model

Organism

Observed Phenotype

schip1

Danio rerio

Structure: pronephric capsular space

Quality: dilated

abnormal

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

Mesodermal Commitment Pathway
Ectoderm Differentiation

Molecular Function

protein binding
identical protein binding

Cellular Component

cytoplasm

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000445224
Coding exons: 7
Length: 57500
Individuals with no LoFs: 0
Homozygous LoFs: 0
Heterozygous LoFs: 0
Defined: 0
p: 0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	1.90	68	129	0.528	0.00000596	1664
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0	0.0	absent
Latino/Admixed American	0	0.0	absent
Ashkenazi Jewish	0	0.0	absent
East Asian	0	0.0	absent
Finnish	0	0.0	absent
European (Non-Finnish)	0	0.0	absent
South Asian	0	0.0	absent
Other	0	0.0	absent

dbNSFP Gene Annotations

Source: dbNSFP

Recessive Scores

pRec: 0.113

Intolerance Scores

RVIS EVS: -0.1
RVIS percentile EVS: 46.49

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: E
Indispensability score: 0.924

Gene Damage Prediction

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