REDIC1

Summary

REDIC1 (regulator of DNA class I crossover intermediates 1, HGNC:26846) is a protein-coding gene on chromosome 12q12, encoding Regulator of DNA class I crossover intermediates 1 (Q86WS4). Involved in recombination, probably acting by stabilizing recombination intermediates during meiotic crossover formation.

Predicted to enable DNA binding activity and RNA binding activity. Predicted to be involved in meiotic cell cycle. Predicted to be located in chromosome.

Source: NCBI Gene 283461 — RefSeq curated summary.

At a glance

• GWAS associations: 1
• Clinical variants (ClinVar): 39 total — 1 pathogenic
• MANE Select transcript: NM_001031748

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:26846
Approved symbol	REDIC1
Name	regulator of DNA class I crossover intermediates 1
Location	12q12
Locus type	gene with protein product
Status	Approved
Aliases	FLJ40126
Ensembl gene	ENSG00000180116
Ensembl biotype	protein_coding
OMIM	620495
Entrez	283461

Gene structure

Transcript identifiers

Ensembl transcripts: 3 — 2 protein_coding, 1 nonsense_mediated_decay

ENST00000324616, ENST00000405531, ENST00000468200

RefSeq mRNA: 2 — MANE Select: NM_001031748 NM_001031748, NM_001319247

CCDS: CCDS41770, CCDS81681

Canonical transcript exons

ENST00000324616 — 13 exons

Exon	Start	End
ENSE00001334919	39720787	39721914
ENSE00001921656	39626183	39626359
ENSE00003245189	39647792	39647977
ENSE00003262877	39646840	39646888
ENSE00003350125	39683415	39683484
ENSE00003384437	39650239	39650354
ENSE00003399665	39682611	39683140
ENSE00003488211	39692049	39692112
ENSE00003524907	39646329	39646461
ENSE00003540010	39640955	39640994
ENSE00003541782	39716756	39716838
ENSE00003571129	39643779	39643917
ENSE00003628713	39684867	39684927

Expression profiles

Bgee: expression breadth broad, 24 present calls, max score 78.30.

FANTOM5 (CAGE): breadth tissue_specific, TPM avg 0.1365 / max 29.3205, expressed in 32 samples.

FANTOM5 promoters (2 alternative TSS)

Promoter ID	TPM avg	Samples expressed
125023	0.1237	30
125024	0.0128	8

Top tissues by expression

220 total, by Bgee expression score (0-100, higher = more expressed):

Tissue	Anatomy ID	Expression score	Quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	78.30	gold quality
secondary oocyte	CL:0000655	75.63	gold quality
sperm	CL:0000019	74.36	silver quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	73.50	gold quality
oocyte	CL:0000023	67.63	gold quality
right testis	UBERON:0004534	64.47	gold quality
testis	UBERON:0000473	63.83	gold quality
left testis	UBERON:0004533	63.25	gold quality
skeletal muscle tissue of rectus abdominis	UBERON:0004511	60.17	gold quality
heart right ventricle	UBERON:0002080	57.88	gold quality
nasal cavity epithelium	UBERON:0005384	56.97	gold quality
endothelial cell	CL:0000115	54.70	gold quality
skeletal muscle tissue of biceps brachii	UBERON:0004502	54.65	gold quality
colonic epithelium	UBERON:0000397	54.33	gold quality
myocardium	UBERON:0002349	53.77	gold quality
lower lobe of lung	UBERON:0008949	51.93	silver quality
postcentral gyrus	UBERON:0002581	50.42	gold quality
cardia of stomach	UBERON:0001162	49.52	gold quality
parietal lobe	UBERON:0001872	49.01	gold quality
vastus lateralis	UBERON:0001379	48.49	gold quality
quadriceps femoris	UBERON:0001377	48.30	gold quality
entorhinal cortex	UBERON:0002728	48.10	gold quality
skeletal muscle tissue	UBERON:0001134	47.53	gold quality
sural nerve	UBERON:0015488	47.26	gold quality
amniotic fluid	UBERON:0000173	47.25	silver quality
tonsil	UBERON:0002372	46.45	gold quality
muscle tissue	UBERON:0002385	46.27	gold quality
superior frontal gyrus	UBERON:0002661	45.97	gold quality
biceps brachii	UBERON:0001507	45.41	gold quality
tendon of biceps brachii	UBERON:0008188	45.40	gold quality

Single-cell (SCXA)

Detected in 1 experiment(s), a significant marker in 1.

Experiment	Marker?	Max mean expression
E-ANND-3	yes	5.51

Regulation

Is transcription factor: no

Cross-species orthologs

2 orthologs

Organism	Symbol	Gene ID
mus_musculus	Redic1	ENSMUSG00000078932
rattus_norvegicus	Redic1	ENSRNOG00000025898

Protein

Protein identifiers

Regulator of DNA class I crossover intermediates 1 — Q86WS4 (reviewed: Q86WS4)

All UniProt accessions (2): A0A0K0K1J7, Q86WS4

UniProt curated annotations — full annotation on UniProt →

Function. Involved in recombination, probably acting by stabilizing recombination intermediates during meiotic crossover formation. Required for normal germline development and fertility. Required for meiotic progression, complete chromosomal synapsis and crossover formation. Binds double-stranded DNA. However, also binds branched DNA molecules, such as those containing a D-loop or Holliday junction structure. Probably not required for formation of DNA double-strand breaks (DSBs). Also binds RNA in an RNA structure-independent manner, with a preference for binding 3’-UTR regions of mRNAs; may stabilize bound RNAs.

Subunit / interactions. Interacts with MSH5. Interacts with TEX11.

Subcellular location. Chromosome.

Disease relevance. Defects in this gene may cause non-obstructive azoospermia.

Miscellaneous. Incomplete or abnormal chromosome synapsis and significantly fewer MLH1 foci observed in spermatocytes from a case of non-obstructive azoospermia.

Isoforms (3)

UniProt ID	Names	Canonical?
Q86WS4-1	1	yes
Q86WS4-2	2
Q86WS4-3	3, HEL-206

RefSeq proteins (2): NP_001026918, NP_001306176 (=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR027883	Redic1-like	Family

Pfam: PF15089

UniProt features (14 total): splice variant 5, compositionally biased region 4, region of interest 2, chain 1, DNA-binding region 1, sequence variant 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q86WS4-F1	43.36	0.00

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 27 (showing top): chr12q12, GOBP_MEIOTIC_CELL_CYCLE, ZNF766_TARGET_GENES, MIR153_5P, MIR548AJ_3P_MIR548X_3P, MIR548AE_3P_MIR548AQ_3P, MIR548AH_3P_MIR548AM_3P, MIR548J_3P, MIR1305, MIR1283, MIR29B_3P_MIR29C_3P, MIR29A_3P, MIR155_5P, MIR552_5P, MIR4451

GO Biological Process (1): meiotic cell cycle (GO:0051321)

GO Molecular Function (3): DNA binding (GO:0003677), RNA binding (GO:0003723), protein binding (GO:0005515)

GO Cellular Component (1): chromosome (GO:0005694)

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
nucleic acid binding	2
cell cycle	1
sexual reproduction	1
reproductive process	1
meiotic nuclear division	1
binding	1
intracellular membraneless organelle	1

Protein interactions and networks

STRING

246 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
REDIC1	C9orf43	Q8TAL5	671
REDIC1	SPATA31G1	Q5VYM1	667
REDIC1	TMCO5A	Q8N6Q1	628
REDIC1	FAM209A	Q5JX71	627
REDIC1	MAGEB16	A2A368	614
REDIC1	TULP2	O00295	595
REDIC1	C3orf80	F5H4A9	595
REDIC1	PKDREJ	Q9NTG1	594
REDIC1	SPATA16	Q9BXB7	574
REDIC1	ZFAND4	Q86XD8	545
REDIC1	CATSPER1	Q8NEC5	534
REDIC1	PTPRQ	Q9UMZ3	505
REDIC1	RPP21	Q9H633	480
REDIC1	WBP2NL	Q6ICG8	464
REDIC1	ESX1	Q8N693	455

IntAct

17 interactions, top by confidence:

A	B	Type	Score
REDIC1	DYNLL2	psi-mi:“MI:0915”(physical association)	0.670
DYNLL2	REDIC1	psi-mi:“MI:0915”(physical association)	0.670
DYNLL1	REDIC1	psi-mi:“MI:0915”(physical association)	0.560
LMO4	REDIC1	psi-mi:“MI:0915”(physical association)	0.560
TNPO2	REDIC1	psi-mi:“MI:0915”(physical association)	0.560
REDIC1	NXF1	psi-mi:“MI:0915”(physical association)	0.560
DYNLL1	REDIC1	psi-mi:“MI:0915”(physical association)	0.000
LMO4	REDIC1	psi-mi:“MI:0915”(physical association)	0.000
NXF1	REDIC1	psi-mi:“MI:0915”(physical association)	0.000
TNPO2	REDIC1	psi-mi:“MI:0915”(physical association)	0.000

BioGRID (6): C12orf40 (Two-hybrid), C12orf40 (Two-hybrid), C12orf40 (Two-hybrid), C12orf40 (Two-hybrid), C12orf40 (Two-hybrid), C12orf40 (Negative Genetic)

ESM2 similar proteins: A0A087WRU1, A0JNH1, A2RUB1, A6QNQ6, B0S6S9, B1WC58, D3Z987, D3ZJ47, E1BC15, O60673, P28358, P28359, P56716, P70347, Q0P5X5, Q0VAV2, Q0VBV7, Q15468, Q2M2Z5, Q3UXL4, Q3V089, Q49A88, Q569L8, Q5BQN8, Q5CZC0, Q5QGS0, Q5T1N1, Q5VWN6, Q60988, Q61493, Q62924, Q6ZP01, Q6ZU52, Q6ZVD7, Q80U59, Q80WQ8, Q86WS4, Q86YC2, Q8CB14, Q8IUR6

Diamond homologs: A0A087WRU1, Q86WS4

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

39 variants total. Per-class counts are floors (≥ shown; pagination cap):

Classification	Count (floor)
Pathogenic	1
Likely pathogenic	0
Uncertain significance	29
Likely benign	1
Benign	0

Top pathogenic / likely-pathogenic (1)

Variant ID	HGVS	Classification
1727243	NM_001031748.4(REDIC1):c.233_234insTT (p.Met78fs)	Pathogenic

SpliceAI

3481 predictions. Top by Δscore:

Variant	Effect	Δscore
12:39640995:GTAA:G	donor_loss	1.0000
12:39642293:GC:G	donor_gain	1.0000
12:39646462:G:GG	donor_gain	1.0000
12:39646836:T:G	acceptor_gain	1.0000
12:39646838:A:AG	acceptor_gain	1.0000
12:39646839:G:GG	acceptor_gain	1.0000
12:39646839:GT:G	acceptor_gain	1.0000
12:39646839:GTGTA:G	acceptor_gain	1.0000
12:39647790:A:AG	acceptor_gain	1.0000
12:39647791:G:GG	acceptor_gain	1.0000
12:39650276:A:G	acceptor_gain	1.0000
12:39683413:A:G	acceptor_gain	1.0000
12:39683485:G:GG	donor_gain	1.0000
12:39716837:TGGTA:T	donor_loss	1.0000
12:39716838:GGT:G	donor_loss	1.0000
12:39716839:G:GG	donor_gain	1.0000
12:39716839:G:T	donor_loss	1.0000
12:39716840:T:TC	donor_loss	1.0000
12:39716841:AA:A	donor_loss	1.0000
12:39760071:T:TA	donor_gain	1.0000
12:39760072:C:A	donor_gain	1.0000
12:39760101:C:CA	donor_gain	1.0000
12:39760135:AG:A	donor_gain	1.0000
12:39760162:T:A	donor_gain	1.0000
12:39764454:TCTTA:T	donor_loss	1.0000
12:39764455:CTTA:C	donor_loss	1.0000
12:39764456:TTA:T	donor_loss	1.0000
12:39764457:TACCA:T	donor_loss	1.0000
12:39764458:A:AC	donor_gain	1.0000
12:39764458:A:AT	donor_loss	1.0000

AlphaMissense

4405 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
12:39626343:T:A	W3R	0.994
12:39626343:T:C	W3R	0.994
12:39626345:G:C	W3C	0.994
12:39626345:G:T	W3C	0.994
12:39643857:A:C	S48R	0.989
12:39643859:C:A	S48R	0.989
12:39643859:C:G	S48R	0.989
12:39643876:T:C	L54P	0.989
12:39640985:A:C	R18S	0.988
12:39640985:A:T	R18S	0.988
12:39626349:G:A	G5R	0.983
12:39626349:G:C	G5R	0.983
12:39626350:G:A	G5E	0.980
12:39643785:T:C	F24L	0.980
12:39643787:T:A	F24L	0.980
12:39643787:T:G	F24L	0.980
12:39626349:G:T	G5W	0.979
12:39640961:G:C	R10S	0.976
12:39640961:G:T	R10S	0.976
12:39626342:T:A	N2K	0.975
12:39626342:T:G	N2K	0.975
12:39626352:G:A	G6R	0.975
12:39626352:G:C	G6R	0.975
12:39640991:A:C	Q20H	0.973
12:39640991:A:T	Q20H	0.973
12:39626359:G:C	R8P	0.971
12:39640973:G:C	K14N	0.970
12:39640973:G:T	K14N	0.970
12:39643863:G:C	D50H	0.969
12:39643864:A:T	D50V	0.969

dbSNP variants (sampled 300 via entrez): RS1000004057 (12:39669226 G>A), RS1000014078 (12:39670734 T>G), RS1000014302 (12:39725721 T>C), RS1000015162 (12:39870238 A>G), RS1000035212 (12:39669439 C>T), RS1000046479 (12:39751616 G>A), RS1000057717 (12:39744186 T>C), RS1000078081 (12:39705654 A>G), RS1000081012 (12:39785237 C>G), RS1000084068 (12:39845009 T>C), RS1000119757 (12:39844774 C>T), RS1000127564 (12:39778613 C>G,T), RS1000130168 (12:39713227 T>C), RS1000144367 (12:39889510 C>T), RS1000145358 (12:39761939 C>T)

Disease associations

OMIM: gene MIM:620495 | disease phenotypes: MIM:258150

GenCC curated gene-disease

Mondo (1): spermatogenic failure (MONDO:0004983)

Orphanet (0):

HPO phenotypes

0 total (0 of 0 shown, HPO-id order):

GWAS associations

1 associations (top):

Study	Trait	p-value
GCST003922_3	Parkinson’s disease	8.000000e-12

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

PharmGKB: 1 entry (VIP=true, CPIC=false)

PharmGKB variants

1 variants.

Variant	Genes	Level	Score	#Clin annots	Drugs
rs10783969	REDIC1		0.00	0

CTD chemical–gene interactions

8 total (human), top 8 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
bisphenol F	affects cotreatment, decreases methylation	1
mivebresib	decreases expression	1
bisphenol A	affects cotreatment, increases methylation	1
2-amino-4-chlorophenol	affects response to substance	1
Fulvestrant	affects cotreatment, increases methylation, decreases methylation	1
Benzo(a)pyrene	decreases methylation	1
Malathion	decreases expression	1
Permethrin	decreases expression	1

Clinical trials (associated diseases)

0 trials via MONDO — disease-level, not drug-specific.