REPS2

RALBP1 associated Eps domain containing 2, the group of EF-hand domain containing

Basic information

Region (hg38): X:16946658-17153272

Links

ENSG00000169891 ∙ NCBI:9185 ∙ OMIM:300317 ∙ HGNC:9963 ∙ Uniprot:Q8NFH8 ∙ 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 REPS2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the REPS2 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				4	1	5
missense			25	3		28
nonsense			1			1
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	26	7	1

Variants in REPS2

This is a list of pathogenic ClinVar variants found in the REPS2 region.

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

Position	Type	Phenotype	Significance	ClinVar
X-16946875-C-T		not specified	Uncertain significance (Dec 30, 2023)
X-16946887-C-T		not specified	Uncertain significance (Aug 01, 2024)
X-16946900-A-G			Likely benign (Dec 31, 2019)
X-16946902-C-T		not specified	Uncertain significance (Mar 20, 2023)
X-16946971-G-A		not specified	Uncertain significance (Mar 13, 2023)
X-16946991-C-G		not specified	Uncertain significance (Feb 28, 2023)
X-16947021-G-C			Uncertain significance (Jan 01, 2023)
X-16947022-G-C		not specified	Uncertain significance (Aug 21, 2023)
X-16947040-C-T			Likely benign (Apr 09, 2018)
X-16947061-C-G		not specified	Uncertain significance (Jun 03, 2022)
X-16947078-G-A			Likely benign (Jul 31, 2018)
X-16947130-A-G		not specified	Uncertain significance (Apr 18, 2023)
X-17006251-G-T		not specified	Uncertain significance (Nov 11, 2024)
X-17006323-C-T		not specified	Uncertain significance (Mar 01, 2023)
X-17022137-C-T		not specified	Uncertain significance (Aug 20, 2024)
X-17022195-A-G		not specified	Uncertain significance (Feb 05, 2024)
X-17022213-T-G		not specified	Uncertain significance (Aug 05, 2024)
X-17022249-G-C		not specified	Uncertain significance (Apr 26, 2023)
X-17022254-G-A		not specified	Uncertain significance (Aug 05, 2023)
X-17025078-C-T		not specified	Uncertain significance (Jul 16, 2024)
X-17025111-C-T		not specified	Uncertain significance (Feb 27, 2023)
X-17029552-G-T		not specified	Uncertain significance (Apr 17, 2024)
X-17029557-G-A			Likely benign (Mar 01, 2023)
X-17029561-G-A		not specified	Uncertain significance (Aug 02, 2022)
X-17029574-C-T		not specified	Uncertain significance (Jun 22, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
REPS2	protein_coding	protein_coding	ENST00000357277	18	206582

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.203	0.797	125728	3	4	125735	0.0000278

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.31	174	230	0.757	0.0000180	4232
Missense in Polyphen		41	68.981	0.59436		1147
Synonymous	-0.549	94	87.5	1.07	0.00000691	1336
Loss of Function	3.45	6	24.4	0.246	0.00000179	439

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000403	0.0000403
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.0000625	0.0000462
European (Non-Finnish)	0.0000252	0.0000176
Middle Eastern	0.00	0.00
South Asian	0.000160	0.0000980
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Involved in growth factor signaling through its influence on the Ral signaling pathway.
• Pathway: EGF-EGFR Signaling Pathway;Vesicle-mediated transport;Membrane Trafficking;Clathrin-mediated endocytosis;EGFR1;Cargo recognition for clathrin-mediated endocytosis (Consensus)

Recessive Scores

• pRec: 0.115

Intolerance Scores

• loftool: 0.346
• rvis_EVS: -0.18
• rvis_percentile_EVS: 40.16

Haploinsufficiency Scores

• pHI: 0.360
• hipred: Y
• hipred_score: 0.786
• ghis: 0.522

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.801

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Reps2

Gene ontology

• Biological process: epidermal growth factor receptor signaling pathway;membrane organization;protein-containing complex assembly
• Cellular component: cytosol
• Molecular function: calcium ion binding;protein binding