SCHIP1

Chr 3

schwannomin interacting protein 1

Also known as: SCHIP-1

NCBI Gene: 29970 ENSG00000151967 UniProt: P0DPB3 OMIM: 619206

SCHIP1 enables identical protein binding activity and is predicted to be involved in positive regulation of hippo signaling and various developmental processes including face morphogenesis. Mutations cause autosomal dominant neurodevelopmental disorder with seizures, hypotonia, and brain imaging abnormalities. The gene is highly constrained against loss-of-function variants, consistent with its role in essential developmental pathways.

OMIM ResearchSummary from RefSeq

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]

OMIM ResearchGenerating clinical summary…

Clinical highlights

Interpreting a novel variant

This gene is strongly intolerant of loss-of-function variation in the population, so LoF variants warrant close attention. No curated mechanism annotation is available — see the mechanism card for the computational prediction and its caveats.Based on population constraint only.

Active trials

Pubs (1 yr)

—

P/LP submissions

—

P/LP missense

0.23

LOEUF· LoF intol.

LOF

Mechanism· predicted

Population Genetics & Constraint

gnomAD v4 — loss-of-function & missense intolerance

gnomAD

LoF intolerant — likely haploinsufficient

LoF Constraint?

0.23LOEUF

pLI 0.987

Z-score 3.36

OE 0.00 (0.00–0.23)

Highly constrained

Highly LoF-intolerant (top ~10% of genes)

Missense Constraint?

1.90Z-score

OE missense 0.53 (0.43–0.65)

68 obs / 128.8 exp

Tolerant

Mild missense constraint

Observed / Expected Ratios?

LoF OE?0.00 (0.00–0.23)

0≤0.351.4

Missense OE?0.53 (0.43–0.65)

0≤0.61.4

Synonymous OE?0.90

0≤1.21.6

LoF obs/exp: 0 / 13.2Missense obs/exp: 68 / 128.8Syn Z: 0.54

Background carrier burden — how many people carry a rare variant somewhere in SCHIP1?

gnomAD v4 · ~731k individuals · PASS only

Rare means allele frequency under

Rare missense

1 in 580

225 rare PASS variants

Rare truncating (LoF)

1 in 20,000

21 rare PASS variants

Rare synonymous (reference)

1 in 260

92 rare PASS variants

Truncating variants are far rarer here than missense — that gap, in human units, is what constraint means for SCHIP1. A background rate for each class, not the frequency of any particular variant; thin-coverage exons undercount.

By genetic ancestry · 9 gnomAD groups · rare = under 0.1% in that group

Group	People	Missense	Truncating
European (non-Finnish)	~556k	1 in 630	1 in 15,000
South Asian	~43k	1 in 400	≈ 1 in 14,000
Remaining (unassigned)	~30k	1 in 630	≈ 1 in 15,000
European (Finnish)	~27k	1 in 3,800	none seen
Admixed American	~22k	1 in 310	none seen
African / African American	~21k	1 in 240	none seen
East Asian	~20k	1 in 500	≈ 1 in 9,900
Ashkenazi Jewish	~13k	≈ 1 in 13,000	none seen
Middle Eastern	~2,884	≈ 1 in 2,900	none seen

Each group is summed over the variants that are rare in that group. Grey ≈ figures rest on fewer than five expected carriers — too few to distinguish groups. Differences mostly reflect how many people were sampled and how much variation each ancestry carries, not disease risk.

Exome coverage (gnomAD): All 8 coding exons well covered in gnomAD exomes and genomes.? see exons ↓