RAD51AP2

Summary

RAD51AP2 (RAD51 associated protein 2, HGNC:34417) is a protein-coding gene on chromosome 2p24.2, encoding RAD51-associated protein 2 (Q09MP3).

Part of protein-containing complex.

Source: NCBI Gene 729475 — RefSeq curated summary.

At a glance

• GWAS associations: 3
• Clinical variants (ClinVar): 156 total — 1 pathogenic
• MANE Select transcript: NM_001099218

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:34417
Approved symbol	RAD51AP2
Name	RAD51 associated protein 2
Location	2p24.2
Locus type	gene with protein product
Status	Approved
Aliases	FLJ17540
Ensembl gene	ENSG00000214842
Ensembl biotype	protein_coding
Entrez	729475

Gene structure

Transcript identifiers

Ensembl transcripts: 1 — 1 protein_coding

ENST00000399080

RefSeq mRNA: 2 — MANE Select: NM_001099218 NM_001099218, NM_001321233

CCDS: CCDS42656

Canonical transcript exons

ENST00000399080 — 3 exons

Exon	Start	End
ENSE00001536343	17510579	17510955
ENSE00001536344	17514012	17514092
ENSE00001536345	17515169	17518440

Expression profiles

Bgee: expression breadth broad, 64 present calls, max score 83.45.

FANTOM5 (CAGE): breadth tissue_specific, TPM avg 0.1997 / max 79.9423, expressed in 50 samples.

FANTOM5 promoters (1 alternative TSS)

Promoter ID	TPM avg	Samples expressed
27033	0.1997	50

Top tissues by expression

112 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	83.45	gold quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	80.53	gold quality
right testis	UBERON:0004534	75.06	gold quality
testis	UBERON:0000473	73.04	gold quality
left testis	UBERON:0004533	72.24	gold quality
cortical plate	UBERON:0005343	63.39	gold quality
ventricular zone	UBERON:0003053	58.67	gold quality
lower esophagus mucosa	UBERON:0035834	58.65	gold quality
ganglionic eminence	UBERON:0004023	57.95	gold quality
prefrontal cortex	UBERON:0000451	53.86	gold quality
Brodmann (1909) area 9	UBERON:0013540	53.12	gold quality
superior frontal gyrus	UBERON:0002661	52.40	gold quality
frontal cortex	UBERON:0001870	52.03	gold quality
dorsolateral prefrontal cortex	UBERON:0009834	51.01	gold quality
primary visual cortex	UBERON:0002436	50.97	gold quality
body of pancreas	UBERON:0001150	50.45	gold quality
right frontal lobe	UBERON:0002810	49.40	gold quality
cerebral cortex	UBERON:0000956	49.38	gold quality
esophagus mucosa	UBERON:0002469	48.17	gold quality
right atrium auricular region	UBERON:0006631	47.84	gold quality
anterior cingulate cortex	UBERON:0009835	47.16	gold quality
olfactory segment of nasal mucosa	UBERON:0005386	46.62	gold quality
pancreas	UBERON:0001264	46.32	gold quality
right lobe of liver	UBERON:0001114	46.24	gold quality
right hemisphere of cerebellum	UBERON:0014890	46.10	silver quality
cerebellar cortex	UBERON:0002129	45.51	silver quality
cerebellar hemisphere	UBERON:0002245	45.44	silver quality
cerebellum	UBERON:0002037	45.25	silver quality
heart left ventricle	UBERON:0002084	45.13	gold quality
liver	UBERON:0002107	44.73	silver quality

Single-cell (SCXA)

Detected in 1 experiment(s), a significant marker in 0.

Experiment	Marker?	Max mean expression
E-ANND-3	no	2.75

Regulation

Is transcription factor: no

Literature-anchored findings (GeneRIF, showing 1)

• A novel protein, RAD51AP2, has been discovered that interacts with RAD51 through a C-terminal motif also present in RAD51AP1. (PMID:16990250)

Cross-species orthologs

2 orthologs

Organism	Symbol	Gene ID
mus_musculus	Rad51ap2	ENSMUSG00000086022
rattus_norvegicus	Rad51ap2	ENSRNOG00000049271

Protein

Protein identifiers

RAD51-associated protein 2 — Q09MP3 (reviewed: Q09MP3)

All UniProt accessions (1): Q09MP3

UniProt curated annotations — full annotation on UniProt →

Subunit / interactions. Interacts with RAD51.

Tissue specificity. Specifically expressed in meiotic tissues. Highly expressed in testis.

RefSeq proteins (2): NP_001092688, NP_001308162 (=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR031419	RAD51_interact	Domain
IPR053355	RAD51-associated	Family

Pfam: PF15696

UniProt features (8 total): sequence variant 3, region of interest 2, mutagenesis site 2, chain 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q09MP3-F1	33.74	0.00

Functional residue map

Curated UniProt residues grouped by drug-discovery relevance — catalytic, ligand-binding, modification, and mutation-validated positions. Source: UniProtKB sequence features.

Mutagenesis-validated functional residues (2):

Position	Phenotype
1134	strongly decreases interaction with rad51; when associated with 1143-aa-1144.
1143–1144	strongly decreases interaction with rad51; when associated with a-1134.

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 24 (showing top): BARX1_TARGET_GENES, CBX7_TARGET_GENES, FOXD2_TARGET_GENES, HDAC4_TARGET_GENES, SALL4_TARGET_GENES, SOX3_TARGET_GENES, ZNF512_TARGET_GENES, ZSCAN5B_TARGET_GENES, MIR616_5P, MIR371B_5P, MIR373_5P, MIR570_3P, MIR4668_3P, MIR6083, MIR2052

GO Biological Process (0):

GO Molecular Function (1): protein binding (GO:0005515)

GO Cellular Component (1): protein-containing complex (GO:0032991)

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
binding	1
cellular_component	1

Protein interactions and networks

STRING

442 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
RAD51AP2	RAD51AP1	Q96B01	493
RAD51AP2	TEX29	Q8N6K0	479
RAD51AP2	DNPH1	O43598	452
RAD51AP2	SYCE3	A1L190	451
RAD51AP2	SYCP1	Q15431	440
RAD51AP2	SYCP3	Q8IZU3	436
RAD51AP2	SPO11	Q9Y5K1	434
RAD51AP2	HORMAD1	Q86X24	433
RAD51AP2	NME8	Q8N427	431
RAD51AP2	H0YEC1	H0YEC1	429
RAD51AP2	MSH4	O15457	413
RAD51AP2	HORMAD2	Q8N7B1	408
RAD51AP2	MEIOB	Q8N635	401
RAD51AP2	TEX11	Q8IYF3	393
RAD51AP2	STRA8	Q7Z7C7	389

IntAct

3 interactions, top by confidence:

A	B	Type	Score
RAD51AP2	ZNF638	psi-mi:“MI:0915”(physical association)	0.400
KLHL22	TRAV18	psi-mi:“MI:0914”(association)	0.350

BioGRID (8): RAD51AP2 (Two-hybrid), RAD51 (Affinity Capture-Western), RAD51 (Two-hybrid), ZNF638 (Proximity Label-MS), RAD51AP2 (Proximity Label-MS), RAD51AP2 (Cross-Linking-MS (XL-MS)), RAD51AP2 (Affinity Capture-MS), RAD51AP2 (Cross-Linking-MS (XL-MS))

ESM2 similar proteins: A0A087WXM9, A0A140LI88, A2AKY4, A4D1E1, A4IGL8, E5FYH0, E9Q3S4, F6ULY3, F7DF15, G3S077, G7H7V7, G7NY55, O13859, O35923, O54952, O88491, P38299, P38398, P46013, P48754, P51587, P97929, Q09MP3, Q28DZ0, Q4V7J0, Q56UN5, Q5DTW7, Q5F2C3, Q5VWN6, Q5VYV7, Q6J6I8, Q6J6J0, Q6NS59, Q77PU6, Q7TSY8, Q7Z570, Q864S8, Q86TB3, Q86XD8, Q8N7Z5

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	1
Likely pathogenic	0
Uncertain significance	137
Likely benign	14
Benign	0

Top pathogenic / likely-pathogenic (1)

Variant ID	HGVS	Classification
4277339	NM_001099218.3(RAD51AP2):c.2985del (p.Asn995fs)	Pathogenic

SpliceAI

582 predictions. Top by Δscore:

Variant	Effect	Δscore
2:17510952:CTAC:C	acceptor_gain	1.0000
2:17514013:T:TA	donor_gain	1.0000
2:17510953:TAC:T	acceptor_gain	0.9900
2:17510954:ACCT:A	acceptor_loss	0.9900
2:17510956:C:CC	acceptor_gain	0.9900
2:17510957:T:C	acceptor_loss	0.9900
2:17512755:C:CT	donor_gain	0.9900
2:17512756:T:TT	donor_gain	0.9900
2:17518223:C:CA	donor_gain	0.9900
2:17512794:T:TA	donor_gain	0.9800
2:17518121:T:C	donor_gain	0.9800
2:17510962:A:AC	acceptor_gain	0.9700
2:17510962:A:C	acceptor_gain	0.9700
2:17514010:ACCT:A	donor_gain	0.9700
2:17514011:CCTC:C	donor_gain	0.9700
2:17514038:T:TA	donor_gain	0.9700
2:17518128:C:A	donor_gain	0.9700
2:17518223:CCCAG:C	donor_gain	0.9700
2:17514090:AATC:A	acceptor_loss	0.9600
2:17514091:ATC:A	acceptor_loss	0.9600
2:17514092:TCTG:T	acceptor_loss	0.9600
2:17514093:CT:C	acceptor_loss	0.9600
2:17514094:T:C	acceptor_loss	0.9600
2:17518127:T:TA	donor_gain	0.9600
2:17518290:T:TA	donor_gain	0.9600
2:17510954:AC:A	acceptor_gain	0.9500
2:17510955:CC:C	acceptor_gain	0.9500
2:17514093:C:CC	acceptor_gain	0.9500
2:17514095:G:C	acceptor_loss	0.9500
2:17518198:C:A	donor_gain	0.9500

AlphaMissense

7840 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
2:17515492:A:G	L975P	0.986
2:17515482:A:C	F978L	0.985
2:17515482:A:T	F978L	0.985
2:17515484:A:G	F978L	0.985
2:17515512:A:C	F968L	0.984
2:17515512:A:T	F968L	0.984
2:17515514:A:G	F968L	0.984
2:17510883:A:G	L1134S	0.963
2:17510916:A:T	L1123H	0.957
2:17515501:A:G	L972P	0.953
2:17510852:A:C	H1144Q	0.952
2:17510852:A:T	H1144Q	0.952
2:17510886:C:T	G1133D	0.948
2:17515483:A:G	F978S	0.945
2:17510916:A:G	L1123P	0.943
2:17515495:T:A	E974V	0.939
2:17510891:C:A	R1131S	0.936
2:17510891:C:G	R1131S	0.936
2:17515470:A:C	S982R	0.936
2:17515470:A:T	S982R	0.936
2:17515472:T:G	S982R	0.936
2:17515492:A:T	L975H	0.933
2:17510887:C:G	G1133R	0.925
2:17510853:T:C	H1144R	0.919
2:17510876:T:A	R1136S	0.918
2:17510876:T:G	R1136S	0.918
2:17515483:A:C	F978C	0.915
2:17510895:A:T	I1130N	0.911
2:17510895:A:G	I1130T	0.905
2:17510895:A:C	I1130S	0.902

dbSNP variants (sampled 300 via entrez): RS1000050809 (2:17538792 T>G), RS1000183155 (2:17511288 C>A), RS1000390705 (2:17529541 C>T), RS1000501380 (2:17526664 T>G), RS1000630777 (2:17519741 G>T), RS1000631262 (2:17513098 T>C), RS1001057808 (2:17526972 A>C), RS1001068983 (2:17536048 T>C), RS1001080306 (2:17536273 C>T), RS1001349015 (2:17530615 A>C), RS1001389971 (2:17532725 G>C), RS1001435312 (2:17533172 C>A), RS1001511131 (2:17523847 G>A), RS1001550060 (2:17524124 C>A), RS1001663435 (2:17531291 C>T)

Disease associations

OMIM: gene `` | disease phenotypes: MIM:620547

GenCC curated gene-disease

Mondo (1): spermatogenic failure 88 (MONDO:0957821)

Orphanet (0):

HPO phenotypes

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

GWAS associations

3 associations (top):

Study	Trait	p-value
GCST001521_37	Subcutaneous adipose tissue	9.000000e-06
GCST003487_17	Response to fenofibrate (total cholesterol levels)	5.000000e-06
GCST009391_177	Metabolite levels	5.000000e-06

EFO canonical traits (2, from GWAS)

EFO ID	Trait name
EFO:0007806	total cholesterol change measurement
EFO:0010476	dimethylglycine measurement

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

6 total (human), top 6 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
Resveratrol	affects cotreatment, decreases expression	1
Benzo(a)pyrene	decreases methylation	1
Copper	affects cotreatment, decreases expression	1
Valproic Acid	decreases methylation	1
Okadaic Acid	decreases expression	1
Lactic Acid	increases expression	1

Clinical trials (associated diseases)

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