CAPN15

protein-coding

calpain 15, the group of MicroRNA protein coding host genes|Zinc fingers RANBP2-type |Calpains

Gene summary

This gene encodes a protein containing zinc-finger-like repeats and a calpain-like protease domain. The encoded protein may function as a transcription factor, RNA-binding protein, or in protein-protein interactions during visual system development. [provided by RefSeq, Jul 2008]

Previous symbols:

SOLH

MANE transcript

NM_005632.3

Inheritance

ClinVar variants

P:10U:269B:123

Top phenotype

Oculogastrointestinal neurodevelopmental syndrome

gnomAD constraint

pLI —, LoF o/e 0.17

Max pathogenic AF

—

Genomic locus

chr16:527,712-554,636

External References & Databases

Ensembl (ENSG00000103326)

Transcript & Mutation Effects

hg38 • Region Span ~26.9 kb

Loading mutation effect viewer...

GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

oculogastrointestinal-neurodevelopmental syndromeSTRONG

Inheritance Pattern: AR

Disease ID:MONDO:0036189

Submitter: G2P

oculogastrointestinal-neurodevelopmental syndromeSTRONG

Inheritance Pattern: AR

Disease ID:MONDO:0036189

Submitter: Labcorp Genetics (formerly Invitae)

Clinical Genomic Database (CGD)

Oculogastrointestinal neurodevelopmental syndromeAR

Manifestation: Audiologic/Otolaryngologic; Cardiovascular; Craniofacial; Gastrointestinal; Musculoskeletal; Neurologic; Ophthalmologic; Renal

Intervention: Cardiovascular

Rationale: Individuals have been described with congenital heart anomalies, and awareness may enable early diagnosis and management

Refs: 32885237; 33410501

Source: CGD (NHGRI)

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to CAPN15 variants in ClinVar

4 Conditions Cataloged

not specifiedTotal: 312

not providedTotal: 88

CAPN15-related disorderTotal: 66

Oculogastrointestinal-neurodevelopmental syndromeTotal: 20

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_005632.3. 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				91 clinvar	6 clinvar	97
missense	4 clinvar	2 clinvar	261 clinvar	24 clinvar	1 clinvar	292
nonsense		2 clinvar	3 clinvar			5
start loss						0
frameshift		1 clinvar	1 clinvar			2
splice donor/acceptor (+/-2bp)	1 clinvar		4 clinvar	1 clinvar		6
Total	5	5	269	116	7	402

Highest pathogenic variant AF is 0.000026469374

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 48 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_005632.3	RefSeq	NP_005623.1	11	MANE Select
ENST00000219611.7	Ensembl	ENSP00000219611.2	11	MANE Select
ENST00000562370.5	Ensembl	ENSP00000456017.1	1	Standard
ENST00000566977.1	Ensembl	ENSP00000457306.1	3	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

Extracellular matrix organization
Degradation of the extracellular matrix

Biological Process

proteolysis

Molecular Function

calcium-dependent cysteine-type endopeptidase activity
metal ion binding

Cellular Component

cytoplasm

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000219611
Coding exons: 11
Length: 26920
Individuals with no LoFs: 124318
Homozygous LoFs: 10
Heterozygous LoFs: 974
Defined: 125302
p: 0.00393

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	1.77	578	711	0.813	0.0000519	6848
Missense (PolyPhen)		214	348.22	0.61455		3242
Synonymous	-4.46	447	342	1.31	0.0000292	2314
Loss of Function	4.97	7	41.6	0.168	0.00000222	410

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00091	0.00086	rare
Latino/Admixed American	0.0037	0.0034	notable
Ashkenazi Jewish	0.0072	0.0060	notable
East Asian	0.000055	0.000054	rare
Finnish	0.0015	0.0014	notable
European (Non-Finnish)	0.0069	0.0061	notable
South Asian	0.0013	0.0011	notable
Other	0.0064	0.0059	notable

dbNSFP Gene Annotations

Source: dbNSFP

Recessive Scores

pRec: 0.120

Essentials

Essential (CRISPR): N
Essential (gene trap): N

Gene Damage Prediction

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