SPINT4

protein-coding

serine peptidase inhibitor, Kunitz type 4

Gene summary

Predicted to enable serine-type endopeptidase inhibitor activity. Predicted to be located in extracellular region. [provided by Alliance of Genome Resources, Jul 2025]

Previous symbols:

C20orf137

MANE transcript

NM_178455.3

Inheritance

—

ClinVar variants

U:14B:2

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.45

Max pathogenic AF

—

Genomic locus

chr20:45,722,347-45,725,830

External References & Databases

Ensembl (ENSG00000149651)

Transcript & Mutation Effects

hg38 • Region Span ~3.5 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 SPINT4 variants in ClinVar

1 Conditions Cataloged

not specifiedTotal: 15

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_178455.3. 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			14 clinvar	2 clinvar		16
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	14	2	0	16

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 2 of 2 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_178455.3	RefSeq	NP_848550.1	3	MANE Select
ENST00000279058.4	Ensembl	ENSP00000279058.3	3	MANE Select

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

negative regulation of endopeptidase activity

Molecular Function

serine-type endopeptidase inhibitor activity

Cellular Component

extracellular region

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000279058
Coding exons: 3
Length: 3480
Individuals with no LoFs: 120591
Homozygous LoFs: 0
Heterozygous LoFs: 12
Defined: 120603
p: 0.0000498

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.334	44	50.7	0.868	0.00000252	651
Missense (PolyPhen)		11	13.161	0.8358		177
Synonymous	-0.241	20	18.7	1.07	9.41e-7	169
Loss of Function	1.08	2	4.45	0.449	2.83e-7	59

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	0.00023	0.00023	rare
Finnish	0	0.0	absent
European (Non-Finnish)	0.000072	0.000072	rare
South Asian	0	0.0	absent
Other	0	0.0	absent

dbNSFP Gene Annotations

Source: dbNSFP

Recessive Scores

pRec: 0.0701

Intolerance Scores

LoFtool: 0.727
RVIS EVS: 0.46
RVIS percentile EVS: 78.16

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.319

Gene Damage Prediction

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