RETREG2

reticulophagy regulator family member 2

Basic information

Region (hg38): 2:219176225-219185475

Previous symbols: [ "C2orf17", "FAM134A" ]

Links

ENSG00000144567 ∙ NCBI:79137 ∙ ∙ HGNC:28450 ∙ Uniprot:Q8NC44 ∙ 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 RETREG2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the RETREG2 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				1		1
missense			43			43
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	43	1	0

Variants in RETREG2

This is a list of pathogenic ClinVar variants found in the RETREG2 region.

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

Position	Type	Phenotype	Significance	ClinVar
2-219176251-G-C		not specified	Uncertain significance (Mar 22, 2023)
2-219176252-C-T		not specified	Uncertain significance (Feb 04, 2025)
2-219176261-G-A		not specified	Uncertain significance (Feb 10, 2022)
2-219176282-T-C		not specified	Uncertain significance (Nov 14, 2024)
2-219176770-T-C		not specified	Uncertain significance (Jul 09, 2024)
2-219176816-C-T		not specified	Uncertain significance (Nov 09, 2022)
2-219178431-G-A		not specified	Uncertain significance (Dec 13, 2023)
2-219178465-A-G		not specified	Uncertain significance (May 28, 2024)
2-219178477-A-C		not specified	Uncertain significance (Jul 05, 2024)
2-219178498-T-C		not specified	Uncertain significance (Oct 18, 2021)
2-219178537-G-A		not specified	Uncertain significance (Oct 13, 2023)
2-219178551-C-A		not specified	Uncertain significance (Sep 03, 2024)
2-219178555-C-T		not specified	Uncertain significance (Dec 19, 2022)
2-219178586-G-T		not specified	Uncertain significance (Jul 06, 2021)
2-219178614-G-A		not specified	Uncertain significance (May 26, 2024)
2-219178626-C-G		not specified	Uncertain significance (Jan 09, 2024)
2-219178981-A-G		not specified	Uncertain significance (Aug 12, 2021)
2-219180132-C-T		not specified	Uncertain significance (Jun 05, 2024)
2-219180150-G-A		not specified	Uncertain significance (Dec 21, 2022)
2-219180190-C-T		not specified	Uncertain significance (Feb 13, 2025)
2-219180237-C-G		not specified	Uncertain significance (Jul 26, 2022)
2-219180719-A-T		not specified	Uncertain significance (May 07, 2024)
2-219181067-A-T		not specified	Uncertain significance (Oct 29, 2024)
2-219181119-A-C		not specified	Uncertain significance (Sep 25, 2023)
2-219181124-C-T		not specified	Uncertain significance (Dec 07, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
RETREG2	protein_coding	protein_coding	ENST00000430297	9	9255

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.249	0.751	125736	0	12	125748	0.0000477

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.291	252	265	0.950	0.0000144	3420
Missense in Polyphen		91	116.67	0.77999		1558
Synonymous	-1.30	139	121	1.15	0.00000703	1202
Loss of Function	3.19	5	20.6	0.242	9.52e-7	265

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000578	0.0000578
Ashkenazi Jewish	0.0000992	0.0000992
East Asian	0.0000544	0.0000544
Finnish	0.0000926	0.0000924
European (Non-Finnish)	0.0000352	0.0000352
Middle Eastern	0.0000544	0.0000544
South Asian	0.0000653	0.0000653
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Recessive Scores

• pRec: 0.100

Intolerance Scores

• rvis_EVS: 0.51
• rvis_percentile_EVS: 80.2

Haploinsufficiency Scores

• pHI: 0.377
• hipred: Y
• hipred_score: 0.518
• ghis: 0.456

Essentials

• essential_gene_gene_trap: N

Mouse Genome Informatics

• Gene name: Retreg2

Gene ontology

• Cellular component: integral component of membrane
• Molecular function: protein binding