RETREG3

reticulophagy regulator family member 3

Basic information

Region (hg38): 17:42579512-42610623

Previous symbols: [ "FAM134C" ]

Links

ENSG00000141699 ∙ NCBI:162427 ∙ OMIM:616498 ∙ HGNC:27258 ∙ Uniprot:Q86VR2 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the RETREG3 gene.

• not provided (35 variants)
• Inborn genetic diseases (10 variants)
• not specified (3 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the RETREG3 gene is commonly pathogenic or not.

In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.

Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.

Variant type	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous					2	2
missense			7	1	2	10
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding			10	19	6	35
Total	0	0	17	20	10

Variants in RETREG3

This is a list of pathogenic ClinVar variants found in the RETREG3 region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
17-42581817-T-C		not specified	Uncertain significance (Oct 06, 2022)
17-42581889-G-C		not specified	Uncertain significance (Nov 22, 2023)
17-42581913-G-A		not specified	Uncertain significance (Feb 23, 2023)
17-42581919-C-T		not specified	Uncertain significance (Oct 20, 2021)
17-42581920-G-A		not specified	Uncertain significance (Aug 01, 2023)
17-42581928-C-G		not specified	Uncertain significance (Dec 20, 2022)
17-42581973-G-A		not specified	Uncertain significance (Jun 03, 2022)
17-42581976-G-A		not specified	Uncertain significance (Sep 22, 2022)
17-42582088-C-T		not specified	Uncertain significance (Nov 14, 2023)
17-42582114-G-C		not specified	Uncertain significance (Aug 30, 2021)
17-42582138-C-T		not specified	Uncertain significance (Jun 17, 2022)
17-42582148-A-C		not specified	Uncertain significance (Sep 25, 2023)
17-42582190-C-T		not specified	Uncertain significance (Jul 11, 2023)
17-42582193-C-G		not specified	Uncertain significance (Oct 18, 2021)
17-42582780-T-A		not specified	Uncertain significance (Feb 05, 2024)
17-42582782-C-T		not specified	Uncertain significance (Dec 27, 2023)
17-42583541-T-C		not specified	Uncertain significance (Jul 19, 2023)
17-42583568-G-A		not specified	Uncertain significance (Feb 13, 2024)
17-42583577-C-T		not specified	Uncertain significance (May 30, 2023)
17-42585160-C-T		not specified	Uncertain significance (Sep 25, 2023)
17-42585179-G-A		not specified	Uncertain significance (Oct 31, 2023)
17-42586083-C-T		not specified	Likely benign (May 18, 2023)
17-42586842-G-C		not specified	Uncertain significance (Jan 23, 2024)
17-42587842-G-T		not specified	Uncertain significance (May 24, 2023)
17-42592072-G-C		not specified	Uncertain significance (Nov 16, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
RETREG3	protein_coding	protein_coding	ENST00000309428	9	31111

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.130	0.870	125737	0	11	125748	0.0000437

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.464	259	281	0.922	0.0000155	3021
Missense in 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

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000578	0.0000578
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000620	0.0000615
Middle Eastern	0.00	0.00
South Asian	0.0000660	0.0000653
Other	0.00	0.00

dbNSFP

Source: dbNSFP

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

Intolerance Scores

• rvis_EVS: -0.8
• rvis_percentile_EVS: 12.33

Haploinsufficiency Scores

• pHI: 0.377
• hipred: N
• hipred_score: 0.492
• ghis: 0.557

Essentials

• essential_gene_gene_trap: N

Mouse Genome Informatics

• Gene name: Retreg3
• Phenotype: adipose tissue phenotype (the observable morphological and physiological characteristics of mammalian fat tissue that are manifested through development and lifespan); growth/size/body region phenotype; homeostasis/metabolism phenotype; cardiovascular system phenotype (the observable morphological and physiological characteristics of the mammalian heart, blood vessels, or circulatory system that are manifested through development and lifespan); hematopoietic system phenotype; vision/eye phenotype; limbs/digits/tail phenotype; nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan); skeleton phenotype

Gene ontology

• Biological process: positive regulation of neuron projection development
• Cellular component: integral component of membrane;protein-containing complex
• Molecular function: protein binding