RETREG3

protein-coding

reticulophagy regulator family member 3

Gene summary

Predicted to enable endoplasmic reticulum-autophagosome adaptor activity. Involved in endoplasmic reticulum tubular network organization; positive regulation of neuron projection development; and reticulophagy. Located in endoplasmic reticulum tubular network. Part of protein-containing complex. [provided by Alliance of Genome Resources, Jul 2025]

Previous symbols:

FAM134C

MANE transcript

NM_178126.4

Inheritance

—

ClinVar variants

U:77B:5

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.26

Max pathogenic AF

—

Genomic locus

chr17:42,579,513-42,610,623

External References & Databases

Ensembl (ENSG00000141699)

Transcript & Mutation Effects

hg38 • Region Span ~31.1 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 RETREG3 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 75

not providedTotal: 4

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_178126.4. 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		2 clinvar	3
missense			75 clinvar	1 clinvar	2 clinvar	78
nonsense			1 clinvar			1
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	77	1	4	82

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 27 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_178126.4	RefSeq	NP_835227.1	9	MANE Select
ENST00000309428.10	Ensembl	ENSP00000309432.4	9	MANE Select
ENST00000585726.5	Ensembl	ENSP00000466145.1	2	Standard
ENST00000585894.5	Ensembl	ENSP00000467847.1	8	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

positive regulation of neuron projection development

Molecular Function

protein binding

Cellular Component

integral component of membrane
protein-containing complex

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000309428
Coding exons: 9
Length: 31111
Individuals with no LoFs: 125737
Homozygous LoFs: 0
Heterozygous LoFs: 11
Defined: 125748
p: 0.0000437

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.464	259	281	0.922	0.0000155	3021
Missense (PolyPhen)		83	105.81	0.78441		1285
Synonymous	-0.195	115	112	1.02	0.00000622	988
Loss of Function	3.28	6	22.9	0.262	0.00000125	230

Population LoF Frequency

Population	CAF	p-value	Status
African	0	0.0	absent
Latino/Admixed American	0.000058	0.000058	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0	0.0	absent
Finnish	0	0.0	absent
European (Non-Finnish)	0.000062	0.000062	rare
South Asian	0.000066	0.000065	rare
Other	0	0.0	absent

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: Mediates NRF1-enhanced neurite outgrowth. {ECO:0000269|PubMed:23939472}.;

Intolerance Scores

RVIS EVS: -0.8
RVIS percentile EVS: 12.33

Essentials

Essential (gene trap): N