SHCBP1

protein-coding

SHC binding and spindle associated 1

Gene summary

Predicted to enable SH2 domain binding activity. Predicted to be involved in fibroblast growth factor receptor signaling pathway and regulation of neural precursor cell proliferation. Located in midbody and mitotic spindle. [provided by Alliance of Genome Resources, Jun 2026]

MANE transcript

NM_024745.5

Inheritance

—

ClinVar variants

U:111B:5

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.51

Max pathogenic AF

—

Genomic locus

chr16:46,578,591-46,621,379

External References & Databases

Ensembl (ENSG00000171241)

Transcript & Mutation Effects

hg38 • Region Span ~42.8 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to SHCBP1 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 105

not providedTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_024745.5. 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			1 clinvar	1 clinvar		2
missense			104 clinvar	3 clinvar	1 clinvar	108
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			6 clinvar			6
Total	0	0	111	4	1	116

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 12 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_024745.5	RefSeq	NP_079021.4	13	MANE Select
ENST00000303383.8	Ensembl	ENSP00000306473.3	13	MANE Select
NM_001324318.2	RefSeq	NP_001311247.1	13	Standard
NM_001324319.2	RefSeq	NP_001311248.1	12	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

fibroblast growth factor receptor signaling pathway
regulation of neural precursor cell proliferation

Molecular Function

protein binding
SH2 domain binding

Cellular Component

cytoplasm
spindle
midbody

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000303383
Coding exons: 13
Length: 41073
Individuals with no LoFs: 125646
Homozygous LoFs: 0
Heterozygous LoFs: 101
Defined: 125747
p: 0.000402

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	1.20	295	359	0.822	0.0000179	4445
Missense (PolyPhen)		56	87.806	0.63777		1116
Synonymous	1.77	110	136	0.808	0.00000719	1233
Loss of Function	2.61	17	33.3	0.511	0.00000164	416

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00037	0.00037	rare
Latino/Admixed American	0.00035	0.00035	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0.00072	0.00071	rare
Finnish	0.00024	0.00023	rare
European (Non-Finnish)	0.00045	0.00044	rare
South Asian	0.00046	0.00046	rare
Other	0.00016	0.00016	rare

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: May play a role in signaling pathways governing cellular proliferation, cell growth and differentiation. May be a component of a novel signaling pathway downstream of Shc. Acts as a positive regulator of FGF signaling in neural progenitor cells. {ECO:0000250|UniProtKB:Q9Z179}.;

Recessive Scores

pRec: 0.0996

Intolerance Scores

LoFtool: 0.850
RVIS EVS: -0.49
RVIS percentile EVS: 22.65

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.168

Gene Damage Prediction

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