TPRG1L

protein-coding

tumor protein p63 regulated 1 like

Gene summary

Predicted to enable calmodulin binding activity and identical protein binding activity. Predicted to be involved in regulation of glutamatergic synaptic transmission and regulation of synaptic vesicle exocytosis. Predicted to act upstream of or within calcineurin-NFAT signaling cascade; negative regulation of synaptic transmission; and synaptic vesicle docking. Located in extracellular exosome. [provided by Alliance of Genome Resources, Jun 2026]

Previous symbols:

FAM79A

MANE transcript

NM_182752.4

Inheritance

—

ClinVar variants

U:45B:4

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.88

Max pathogenic AF

—

Genomic locus

chr1:3,625,015-3,630,127

External References & Databases

Ensembl (ENSG00000158109)

Transcript & Mutation Effects

hg38 • Region Span ~5.1 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 TPRG1L variants in ClinVar

1 Conditions Cataloged

not specifiedTotal: 44

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_182752.4. 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			1 clinvar			1
missense			41 clinvar	4 clinvar		45
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			3 clinvar			3
Total	0	0	45	4	0	49

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 11 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_182752.4	RefSeq	NP_877429.2	5	MANE Select
ENST00000378344.7	Ensembl	ENSP00000367595.2	5	MANE Select
ENST00000344579.5	Ensembl	ENSP00000339714.5	4	Standard
ENST00000344579.6	Ensembl	ENSP00000339714.5	4	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

biological_process
regulation of synaptic transmission, glutamatergic

Molecular Function

molecular_function
identical protein binding

Cellular Component

cytoplasm
synaptic vesicle
cell junction
synaptic vesicle membrane
calyx of Held

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000378344
Coding exons: 5
Length: 5126
Individuals with no LoFs: 125365
Homozygous LoFs: 1
Heterozygous LoFs: 381
Defined: 125747
p: 0.00152

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.784	98	122	0.801	0.00000670	1735
Missense (PolyPhen)		40	44.343	0.90206		538
Synonymous	-1.37	62	49.7	1.25	0.00000295	563
Loss of Function	0.372	10	11.4	0.881	5.70e-7	131

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00062	0.00062	rare
Latino/Admixed American	0.00040	0.00040	rare
Ashkenazi Jewish	0.00070	0.00069	rare
East Asian	0.000054	0.000054	rare
Finnish	0.00069	0.00069	rare
European (Non-Finnish)	0.0029	0.0029	notable
South Asian	0.00016	0.00016	rare
Other	0.00082	0.00081	rare

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: Presynaptic protein involved in the synaptic transmission tuning. Regulates synaptic release probability by decreasing the calcium sensitivity of release. {ECO:0000250|UniProtKB:A8WCF8}.;

Recessive Scores

pRec: 0.109

Intolerance Scores

LoFtool: 0.447
RVIS EVS: -0.12
RVIS percentile EVS: 44.89

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: E
Indispensability score: 0.601

Gene Damage Prediction

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