DCAF12L1

Summary

DCAF12L1 (DDB1 and CUL4 associated factor 12 like 1, HGNC:29395) is a protein-coding gene on chromosome Xq25, encoding DDB1- and CUL4-associated factor 12-like protein 1 (Q5VU92).

This gene encodes a member of the WD repeat protein family. WD repeats are minimally conserved regions of approximately 40 amino acids typically bracketed by gly-his and trp-asp (GH-WD), which may facilitate formation of heterotrimeric or multiprotein complexes. Members of this family are involved in a variety of cellular processes, including cell cycle progression, signal transduction, apoptosis, and gene regulation.

Source: NCBI Gene 139170 — RefSeq curated summary.

At a glance

• GWAS associations: 1
• Clinical variants (ClinVar): 61 total — 1 likely-pathogenic
• MANE Select transcript: NM_178470

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:29395
Approved symbol	DCAF12L1
Name	DDB1 and CUL4 associated factor 12 like 1
Location	Xq25
Locus type	gene with protein product
Status	Approved
Aliases	KIAA1892L
Ensembl gene	ENSG00000198889
Ensembl biotype	protein_coding
Entrez	139170

Gene structure

Transcript identifiers

Ensembl transcripts: 1 — 1 protein_coding

ENST00000371126

RefSeq mRNA: 1 — MANE Select: NM_178470 NM_178470

CCDS: CCDS14610

Canonical transcript exons

ENST00000371126 — 2 exons

Exon	Start	End
ENSE00001436827	126549383	126551107
ENSE00001454400	126551195	126552814

Expression profiles

Bgee: expression breadth broad, 61 present calls, max score 84.73.

FANTOM5 (CAGE): breadth tissue_specific, TPM avg 0.2797 / max 47.3639, expressed in 99 samples.

FANTOM5 promoters (1 alternative TSS)

Promoter ID	TPM avg	Samples expressed
200425	0.2797	99

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	84.73	gold quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	83.86	gold quality
caput epididymis	UBERON:0004358	79.29	gold quality
corpus epididymis	UBERON:0004359	78.09	gold quality
cauda epididymis	UBERON:0004360	69.25	gold quality
testis	UBERON:0000473	68.58	gold quality
right testis	UBERON:0004534	68.23	gold quality
left testis	UBERON:0004533	66.44	gold quality
oviduct epithelium	UBERON:0004804	65.47	gold quality
fallopian tube	UBERON:0003889	63.33	gold quality
gall bladder	UBERON:0002110	62.61	gold quality
seminal vesicle	UBERON:0000998	61.86	gold quality
left uterine tube	UBERON:0001303	59.45	gold quality
adult organism	UBERON:0007023	59.01	gold quality
epithelial cell of pancreas	CL:0000083	58.51	silver quality
endometrium	UBERON:0001295	57.80	gold quality
cartilage tissue	UBERON:0002418	57.22	gold quality
cardiac muscle of right atrium	UBERON:0003379	54.34	gold quality
left ventricle myocardium	UBERON:0006566	54.23	gold quality
pancreatic ductal cell	CL:0002079	54.16	silver quality
kidney epithelium	UBERON:0004819	53.93	gold quality
upper arm skin	UBERON:0004263	53.52	gold quality
right uterine tube	UBERON:0001302	53.49	gold quality
adult mammalian kidney	UBERON:0000082	53.37	gold quality
body of stomach	UBERON:0001161	53.04	gold quality
ovary	UBERON:0000992	52.81	gold quality
fundus of stomach	UBERON:0001160	52.67	gold quality
tibialis anterior	UBERON:0001385	52.33	silver quality
metanephros	UBERON:0000081	52.31	gold quality
ventricular zone	UBERON:0003053	52.21	silver quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	no	1.80

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

83 targeting DCAF12L1, top 30 by miRDB confidence (max_score; target_count = how many genes the miRNA targets in total — lower means more specific):

miRNA	Max score	Avg score	miRNA target_count
HSA-MIR-4262	100.00	73.26	3931
HSA-MIR-29A-3P	100.00	73.11	1835
HSA-MIR-29B-3P	100.00	73.18	1833
HSA-MIR-29C-3P	100.00	73.15	1833
HSA-MIR-3925-3P	100.00	69.95	1237
HSA-MIR-6867-5P	100.00	82.21	3464
HSA-MIR-196A-1-3P	99.99	72.15	2772
HSA-MIR-4531	99.99	69.70	3181
HSA-MIR-181A-5P	99.99	72.96	2995
HSA-MIR-181B-5P	99.99	72.97	2996
HSA-MIR-181C-5P	99.99	72.95	2996
HSA-MIR-181D-5P	99.99	73.04	2997
HSA-MIR-513B-5P	99.99	69.96	2150
HSA-MIR-548AJ-3P	99.96	73.38	5345
HSA-MIR-548X-3P	99.96	73.38	5345
HSA-MIR-570-3P	99.96	72.41	4910
HSA-MIR-3910	99.95	71.13	2227
HSA-MIR-548J-3P	99.94	72.61	4881
HSA-MIR-548AE-3P	99.93	72.66	4867
HSA-MIR-548AH-3P	99.93	72.54	4872
HSA-MIR-548AM-3P	99.93	72.54	4872
HSA-MIR-548AQ-3P	99.93	72.66	4867
HSA-MIR-335-3P	99.93	73.36	4958
HSA-MIR-1-3P	99.93	72.35	1914
HSA-MIR-206	99.93	72.50	1893
HSA-MIR-7-1-3P	99.91	71.53	4384
HSA-MIR-7-2-3P	99.91	71.40	4394
HSA-MIR-5680	99.91	69.83	3421
HSA-MIR-374A-5P	99.90	71.34	2923
HSA-MIR-374B-5P	99.90	69.98	2734

Literature-anchored findings (GeneRIF, showing 1)

• Functionally characterizes other DDB1- and CUL4-associated factors, including the DCAF12 factor which most closely resembles the product of this gene. (PMID:16949367)

Cross-species orthologs

0 orthologs

Paralogs (2): DCAF12L2 (ENSG00000198354), DCAF12 (ENSG00000198876)

Protein

Protein identifiers

DDB1- and CUL4-associated factor 12-like protein 1 — Q5VU92 (reviewed: Q5VU92)

Alternative names: WD repeat-containing protein 40B

All UniProt accessions (1): Q5VU92

UniProt curated annotations — full annotation on UniProt →

Similarity. Belongs to the WD repeat DCAF12 family.

RefSeq proteins (1): NP_848565* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR001680	WD40_rpt	Repeat
IPR015943	WD40/YVTN_repeat-like_dom_sf	Homologous_superfamily
IPR036322	WD40_repeat_dom_sf	Homologous_superfamily
IPR051191	DCAF12	Family
IPR056151	Beta-prop_DCAF12	Domain

Pfam: PF23760

UniProt features (9 total): repeat 6, chain 1, region of interest 1, sequence variant 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q5VU92-F1	78.40	0.50

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 58 (showing top): ACATTCC_MIR1_MIR206, TGCCTTA_MIR124A, GOCC_TRANSFERASE_COMPLEX, GOCC_CUL4_RING_E3_UBIQUITIN_LIGASE_COMPLEX, GOCC_CULLIN_RING_UBIQUITIN_LIGASE_COMPLEX, ZHENG_GLIOBLASTOMA_PLASTICITY_DN, RAY_TUMORIGENESIS_BY_ERBB2_CDC25A_UP, GOCC_UBIQUITIN_LIGASE_COMPLEX, ZHOU_INFLAMMATORY_RESPONSE_LIVE_UP, MEISSNER_NPC_HCP_WITH_H3K4ME2, LU_EZH2_TARGETS_DN, chrXq25, KATSANOU_ELAVL1_TARGETS_UP, ZNF618_TARGET_GENES, MIR548AJ_3P_MIR548X_3P

GO Biological Process (0):

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

GO Cellular Component (1): Cul4-RING E3 ubiquitin ligase complex (GO:0080008)

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
binding	1
cullin-RING ubiquitin ligase complex	1

Protein interactions and networks

STRING

444 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
DCAF12L1	DDB1	Q16531	653
DCAF12L1	SH2D2A	Q9NP31	573
DCAF12L1	DCAF8L1	A6NGE4	501
DCAF12L1	DCAF8L2	P0C7V8	474
DCAF12L1	ANKRD20A1	Q5TYW2	444
DCAF12L1	DCAF11	Q8TEB1	429
DCAF12L1	PRR32	B1ATL7	400
DCAF12L1	PRXL2C	Q7RTV5	400
DCAF12L1	PDCL2	Q8N4E4	399
DCAF12L1	TMEM95	Q3KNT9	391
DCAF12L1	FARP1	Q9Y4F1	381
DCAF12L1	LRRC57	Q8N9N7	370
DCAF12L1	NDUFA1	O15239	368
DCAF12L1	CATSPERT	Q53TS8	357
DCAF12L1	GMPR	P36959	329

IntAct

21 interactions, top by confidence:

A	B	Type	Score
CCT2	TXNDC9	psi-mi:“MI:0914”(association)	0.730
PFDN2	POLR3A	psi-mi:“MI:0914”(association)	0.670
DCAF12L2	CETN3	psi-mi:“MI:0914”(association)	0.640
BCL7A	ARID1A	psi-mi:“MI:0914”(association)	0.640
CCT3	TXNDC9	psi-mi:“MI:0914”(association)	0.640
CCT7	TXNDC9	psi-mi:“MI:0914”(association)	0.640
STAMBPL1	PIK3C2A	psi-mi:“MI:0914”(association)	0.640
DCAF12L1	SH2D2A	psi-mi:“MI:0915”(physical association)	0.570
SH2D2A	DCAF12L1	psi-mi:“MI:0915”(physical association)	0.570
DRG1	LRRC41	psi-mi:“MI:0914”(association)	0.530
GPS1	PXDNL	psi-mi:“MI:0914”(association)	0.530
KCTD17	CBX4	psi-mi:“MI:0914”(association)	0.530
ZNRD2	CCDC85C	psi-mi:“MI:0914”(association)	0.530
CNGA3	MAGEA6	psi-mi:“MI:0914”(association)	0.350
COPS2	RHOBTB1	psi-mi:“MI:0914”(association)	0.350
CUL4B	CAND2	psi-mi:“MI:0914”(association)	0.350
TNFRSF6B	FBXO21	psi-mi:“MI:0914”(association)	0.350

BioGRID (6): DCAF12L1 (Two-hybrid), SH2D2A (Affinity Capture-Luminescence), DCAF12L1 (Affinity Capture-MS), DCAF12L1 (Affinity Capture-MS), DCAF12L1 (Affinity Capture-MS), DCAF12L1 (Proximity Label-MS)

ESM2 similar proteins: A1L112, A4IHS2, A8NZM5, B2ZZS9, O00423, O80775, O95834, P93107, P97452, Q05BC3, Q0DYP5, Q13216, Q13610, Q13685, Q15269, Q1JQD2, Q2HJ56, Q32KQ2, Q32P44, Q3SZK1, Q4V8C3, Q562C2, Q58DT8, Q5BIM8, Q5F3K4, Q5R9T6, Q5RCG7, Q5RFQ3, Q5VU92, Q5XI13, Q5ZK69, Q6DRF9, Q6P6T4, Q6PFM9, Q7TNG5, Q7YR70, Q810D6, Q8BH57, Q8BHB4, Q8BU03

Diamond homologs: Q08BB3, Q3MHH0, Q4R3J7, Q5F3R7, Q5T6F0, Q5VU92, Q5VW00, Q63ZP7, Q6AX81, Q6P809, Q8BGW4, Q8BGZ3, Q8CBW4, Q9VGE3, Q9AV81

SIGNOR signaling

0 interactions.

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 29 IntAct physical interaction partners (hypergeometric vs the genome-wide background, BH-FDR, gene-set size 15–500, ranked by fold). A functional readout of the neighbourhood — distinct from this gene’s own memberships above, and biased toward well-studied / hub proteins, so read it as themes rather than proof.

Reactome pathways:

Pathway	Partners	Fold	FDR
RHOBTB1 GTPase cycle	5	125.2×	3e-08
Neddylation	5	12.5×	4e-04

GO biological processes:

GO term	Partners	Fold	FDR
protein stabilization	5	11.9×	1e-03

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	1
Uncertain significance	36
Likely benign	10
Benign	3

Top pathogenic / likely-pathogenic (1)

Variant ID	HGVS	Classification
2690984	NM_178470.5(DCAF12L1):c.406_407del (p.Leu136fs)	Likely pathogenic

SpliceAI

142 predictions. Top by Δscore:

Variant	Effect	Δscore
X:126551220:G:C	donor_gain	0.8700
X:126551189:GTGTA:G	donor_loss	0.8400
X:126551190:TGTAC:T	donor_loss	0.8400
X:126551191:GTA:G	donor_loss	0.8400
X:126551192:TAC:T	donor_loss	0.8400
X:126551193:A:C	donor_loss	0.8400
X:126551194:C:G	donor_loss	0.8400
X:126551195:C:G	donor_loss	0.8200
X:126551214:T:TA	donor_gain	0.7500
X:126551106:AC:A	acceptor_loss	0.6500
X:126551107:CC:C	acceptor_loss	0.6500
X:126551109:T:G	acceptor_loss	0.6500
X:126551110:GGAAA:G	acceptor_loss	0.6400
X:126551111:GAAAA:G	acceptor_loss	0.6400
X:126551116:C:CT	acceptor_loss	0.6400
X:126551117:A:T	acceptor_loss	0.6400
X:126551112:AAAA:A	acceptor_loss	0.6200
X:126551219:AGCT:A	donor_gain	0.6100
X:126551335:T:TA	donor_gain	0.6100
X:126550822:ACT:A	acceptor_gain	0.5800
X:126551353:T:C	donor_gain	0.5700
X:126551132:T:TC	acceptor_loss	0.5600
X:126551408:T:TA	donor_gain	0.5600
X:126551108:C:CC	acceptor_gain	0.5500
X:126551113:AAACA:A	acceptor_loss	0.5500
X:126551114:AACAA:A	acceptor_loss	0.5500
X:126551115:ACAAA:A	acceptor_loss	0.5500
X:126551118:AAAGA:A	acceptor_loss	0.5500
X:126551131:GTTAA:G	acceptor_loss	0.5500
X:126550821:AACT:A	acceptor_gain	0.5400

AlphaMissense

2995 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
X:126552296:A:G	W105R	0.999
X:126552296:A:T	W105R	0.999
X:126551979:G:C	S210R	0.998
X:126551979:G:T	S210R	0.998
X:126551981:T:G	S210R	0.998
X:126552294:C:A	W105C	0.998
X:126552294:C:G	W105C	0.998
X:126552080:A:C	Y177D	0.996
X:126551225:A:G	W462R	0.995
X:126551225:A:T	W462R	0.995
X:126551951:A:G	W220R	0.995
X:126551951:A:T	W220R	0.995
X:126552005:A:G	W202R	0.995
X:126552005:A:T	W202R	0.995
X:126552115:G:T	A165D	0.995
X:126551644:G:T	A322D	0.994
X:126552295:C:G	W105S	0.994
X:126552306:G:C	F101L	0.994
X:126552306:G:T	F101L	0.994
X:126552308:A:G	F101L	0.994
X:126551278:A:G	F444S	0.993
X:126551546:A:G	S355P	0.993
X:126551269:C:T	G447E	0.992
X:126552265:G:A	T115I	0.992
X:126552268:C:T	G114D	0.992
X:126551270:C:A	G447W	0.991
X:126552135:A:C	N158K	0.991
X:126552135:A:T	N158K	0.991
X:126551242:C:T	G456E	0.990
X:126551949:C:A	W220C	0.990

dbSNP variants (sampled 300 via entrez): RS1000127603 (X:126554263 C>T), RS1002390113 (X:126550251 C>A,T), RS1003529531 (X:126551264 G>C), RS1004393150 (X:126554138 T>C), RS1004432170 (X:126552422 A>C), RS1004766582 (X:126553715 T>G), RS1004787363 (X:126551175 T>C,G), RS1005245083 (X:126550490 C>T), RS1006011729 (X:126548905 C>A,G), RS1006505780 (X:126552954 G>A,C,T), RS1007421954 (X:126551018 C>G), RS1008012847 (X:126552845 G>A,C,T), RS1008289158 (X:126553199 C>G), RS1008691300 (X:126549784 A>G), RS1009430124 (X:126554733 A>T)

Disease associations

OMIM: gene `` | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (1): Male infertility with azoospermia or oligozoospermia due to single gene mutation (Orphanet:399805)

HPO phenotypes

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

GWAS associations

1 associations (top):

Study	Trait	p-value
GCST007594_3	Handedness (Right-handed vs. non-right-handed)	1.000000e-08

EFO canonical traits (1, from GWAS)

EFO ID	Trait name
EFO:0009902	handedness

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

14 total (human), top 14 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
Valproic Acid	affects cotreatment, increases expression, affects expression, increases methylation	6
Phenylmercuric Acetate	decreases expression, affects cotreatment	2
aristolochic acid I	decreases expression	1
trichostatin A	increases expression	1
perfluorooctane sulfonic acid	decreases expression	1
4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamide	affects cotreatment, decreases expression, increases expression	1
dorsomorphin	affects cotreatment, decreases expression, increases expression	1
theaflavin-3,3’-digallate	affects expression	1
Resveratrol	decreases expression, affects cotreatment	1
Benzo(a)pyrene	affects methylation, decreases methylation	1
Phthalic Acids	decreases expression	1
Plant Extracts	affects cotreatment, decreases expression	1
8-Bromo Cyclic Adenosine Monophosphate	increases expression	1
Copper Sulfate	increases expression	1

Clinical trials (associated diseases)

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