CRACDL

Summary

CRACDL (CRACD like, HGNC:33454) is a protein-coding gene on chromosome 2q11.2, encoding CRACD-like protein (Q6NV74).

At a glance

• GWAS associations: 5
• Clinical variants (ClinVar): 200 total
• MANE Select transcript: NM_207362

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:33454
Approved symbol	CRACDL
Name	CRACD like
Location	2q11.2
Locus type	gene with protein product
Status	Approved
Aliases	MGC42367
Ensembl gene	ENSG00000196872
Ensembl biotype	protein_coding
Entrez	343990

Gene structure

Transcript identifiers

Ensembl transcripts: 11 — 9 protein_coding, 2 protein_coding_CDS_not_defined

ENST00000397899, ENST00000415261, ENST00000420294, ENST00000423771, ENST00000428096, ENST00000462314, ENST00000464413, ENST00000867238, ENST00000867239, ENST00000867240, ENST00000867241

RefSeq mRNA: 1 — MANE Select: NM_207362 NM_207362

CCDS: CCDS42720

Canonical transcript exons

ENST00000397899 — 10 exons

Exon	Start	End
ENSE00001400222	98832862	98832997
ENSE00001530647	98793846	98794671
ENSE00001530649	98796120	98796264
ENSE00001530650	98797350	98797537
ENSE00001530651	98821857	98823537
ENSE00003461617	98826975	98827169
ENSE00003545767	98838119	98838287
ENSE00003639430	98846731	98846810
ENSE00003790398	98832348	98832512
ENSE00003847353	98935938	98936225

Expression profiles

Bgee: expression breadth ubiquitous, 241 present calls, max score 99.06.

FANTOM5 (CAGE): breadth broad, TPM avg 2.9216 / max 129.4078, expressed in 450 samples.

FANTOM5 promoters (9 alternative TSS)

Promoter ID	TPM avg	Samples expressed
29866	1.6162	209
29862	0.4928	220
29864	0.2954	149
29865	0.1320	52
29868	0.1120	62
29867	0.1088	57
29860	0.0903	38
29861	0.0374	15
29863	0.0368	15

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
bronchial epithelial cell	CL:0002328	99.06	gold quality
middle temporal gyrus	UBERON:0002771	98.86	gold quality
bronchus	UBERON:0002185	98.39	gold quality
Brodmann (1909) area 23	UBERON:0013554	98.14	gold quality
endothelial cell	CL:0000115	97.34	gold quality
corpus epididymis	UBERON:0004359	97.30	gold quality
Brodmann (1909) area 46	UBERON:0006483	95.67	gold quality
entorhinal cortex	UBERON:0002728	95.63	gold quality
superior frontal gyrus	UBERON:0002661	95.60	gold quality
parietal lobe	UBERON:0001872	95.58	gold quality
postcentral gyrus	UBERON:0002581	95.53	gold quality
parotid gland	UBERON:0001831	95.28	gold quality
pancreatic ductal cell	CL:0002079	94.86	gold quality
primary visual cortex	UBERON:0002436	94.28	gold quality
occipital lobe	UBERON:0002021	94.09	gold quality
mucosa of paranasal sinus	UBERON:0005030	93.10	gold quality
nasal cavity epithelium	UBERON:0005384	92.92	gold quality
amniotic fluid	UBERON:0000173	91.68	gold quality
oral cavity	UBERON:0000167	91.25	gold quality
frontal cortex	UBERON:0001870	91.00	gold quality
caput epididymis	UBERON:0004358	90.99	gold quality
dorsolateral prefrontal cortex	UBERON:0009834	90.95	gold quality
right uterine tube	UBERON:0001302	90.45	gold quality
Brodmann (1909) area 9	UBERON:0013540	90.25	gold quality
epithelium of nasopharynx	UBERON:0001951	90.22	gold quality
prefrontal cortex	UBERON:0000451	90.11	gold quality
right frontal lobe	UBERON:0002810	89.89	gold quality
adult organism	UBERON:0007023	89.28	gold quality
cerebral cortex	UBERON:0000956	89.23	gold quality
temporal lobe	UBERON:0001871	89.04	gold quality

Single-cell (SCXA)

Detected in 3 experiment(s), a significant marker in 3.

Experiment	Marker?	Max mean expression
E-HCAD-35	yes	96.77
E-HCAD-25	yes	74.78
E-ANND-3	yes	10.76

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

63 targeting CRACDL, 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-3064-3P	100.00	70.09	1254
HSA-MIR-513A-5P	100.00	69.77	2465
HSA-MIR-30A-5P	100.00	76.31	3233
HSA-MIR-30B-5P	100.00	76.29	3248
HSA-MIR-30C-5P	100.00	76.29	3248
HSA-MIR-30D-5P	100.00	76.32	3233
HSA-MIR-30E-5P	100.00	76.32	3242
HSA-MIR-4776-3P	100.00	68.73	1340
HSA-MIR-4668-3P	100.00	68.74	2635
HSA-MIR-548C-3P	99.99	74.01	7587
HSA-MIR-34A-5P	99.99	71.21	1784
HSA-MIR-449A	99.99	71.05	1776
HSA-MIR-27A-3P	99.98	72.13	2955
HSA-MIR-27B-3P	99.98	72.13	2955
HSA-MIR-9985	99.98	72.11	2939
HSA-MIR-4482-3P	99.98	72.50	3147
HSA-MIR-3148	99.97	75.06	6478
HSA-MIR-34C-5P	99.97	70.45	1577
HSA-MIR-449B-5P	99.97	70.26	1580
HSA-MIR-551B-5P	99.96	71.28	3493
HSA-MIR-128-3P	99.95	71.17	2484
HSA-MIR-216A-3P	99.95	71.19	2505
HSA-MIR-22-3P	99.93	68.13	917
HSA-MIR-3681-3P	99.88	70.46	2254
HSA-MIR-6124	99.87	69.78	3551
HSA-MIR-3681-5P	99.82	66.88	387
HSA-MIR-6875-3P	99.82	70.26	2983
HSA-MIR-132-3P	99.73	70.56	1424
HSA-MIR-212-3P	99.73	70.65	1424
HSA-MIR-548AU-3P	99.70	68.22	1373

Literature-anchored findings (GeneRIF, showing 1)

• Stratified analyses of genome wide association study data reveal haplotypes for a candidate gene on chromosome 2 (KIAA1211L) is associated with opioid use in patients of Arabian descent. (PMID:32005204)

Cross-species orthologs

2 orthologs

Organism	Symbol	Gene ID
mus_musculus	Cracdl	ENSMUSG00000026090
rattus_norvegicus	Cracdl	ENSRNOG00000018366

Paralogs (1): DNAAF3 (ENSG00000167646)

Protein

Protein identifiers

CRACD-like protein — Q6NV74 (reviewed: Q6NV74)

All UniProt accessions (5): Q6NV74, C9JDX0, C9JFM2, C9JK00, C9JXD6

RefSeq proteins (1): NP_997245* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR026713	CRACD-like	Family
IPR028030	DUF4592	Domain

Pfam: PF15262

UniProt features (25 total): compositionally biased region 17, region of interest 3, modified residue 2, chain 1, sequence variant 1, sequence conflict 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q6NV74-F1	50.07	0.02

Functional residue map

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

Post-translational modifications (2): 92, 490

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 122 (showing top): AP1_01, SENGUPTA_NASOPHARYNGEAL_CARCINOMA_DN, BACH2_01, TGANTCA_AP1_C, AACTTT_UNKNOWN, TGTTTAC_MIR30A5P_MIR30C_MIR30D_MIR30B_MIR30E5P, NKX3A_01, CHARAFE_BREAST_CANCER_LUMINAL_VS_MESENCHYMAL_UP, MARSON_BOUND_BY_FOXP3_UNSTIMULATED, WGTTNNNNNAAA_UNKNOWN, chr2q11, DODD_NASOPHARYNGEAL_CARCINOMA_DN, CHEMNITZ_RESPONSE_TO_PROSTAGLANDIN_E2_DN, BHAT_ESR1_TARGETS_NOT_VIA_AKT1_DN, RATTENBACHER_BOUND_BY_CELF1

GO Biological Process (0):

GO Molecular Function (0):

GO Cellular Component (0):

Protein interactions and networks

STRING

1139 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
CRACDL	CCDC166	P0CW27	507
CRACDL	CWH43	Q9H720	505
CRACDL	GIMAP6	Q6P9H5	467
CRACDL	OR6B3	Q8NGW1	445
CRACDL	KIF18A	Q8NI77	407
CRACDL	ZC3H3	Q8IXZ2	403
CRACDL	TCP11L1	Q9NUJ3	398
CRACDL	VWC2L	B2RUY7	372
CRACDL	UNC80	Q8N2C7	370
CRACDL	ERLN	P0DI80	353
CRACDL	ZNF549	Q6P9A3	348
CRACDL	C11orf21	Q9P2W6	348
CRACDL	LMAN1L	Q9HAT1	339
CRACDL	FASTKD1	Q53R41	333
CRACDL	R3HCC1	Q9Y3T6	326
CRACDL	CCDC85C	A6NKD9	326

IntAct

10 interactions, top by confidence:

A	B	Type	Score
CAPZB	CNOT1	psi-mi:“MI:0914”(association)	0.640
CRACDL	EIF4B	psi-mi:“MI:0915”(physical association)	0.400
APP	ESYT2	psi-mi:“MI:0914”(association)	0.350
ESR1	ESYT2	psi-mi:“MI:0914”(association)	0.350
P		psi-mi:“MI:0914”(association)	0.350
ARHGAP35	RASA1	psi-mi:“MI:0914”(association)	0.350
CAPZB	ENAH	psi-mi:“MI:0914”(association)	0.350

BioGRID (10): KIAA1211L (Affinity Capture-MS), KIAA1211L (Proximity Label-MS), KIAA1211L (Proximity Label-MS), KIAA1211L (Affinity Capture-MS), KIAA1211L (Affinity Capture-MS), KIAA1211L (Affinity Capture-MS), KIAA1211L (Affinity Capture-MS), KIAA1211L (Affinity Capture-MS), KIAA1211L (Cross-Linking-MS (XL-MS)), KIAA1211L (Affinity Capture-MS)

ESM2 similar proteins: A0A8I5ZM56, A2AG50, A2AI08, A2AJI0, A5D7K1, D4A4L4, E1C2Q8, F1LR10, O00515, O14529, O75128, O88573, O88735, P51825, P57016, Q14244, Q32LQ1, Q3KQU3, Q3U2K0, Q5JTD0, Q5NBX1, Q5PR69, Q5R7F9, Q5XHX2, Q5ZIA2, Q5ZJJ1, Q68DK7, Q6IPM2, Q6NV74, Q6NZF1, Q6PDH0, Q6PDM1, Q6PG95, Q6ZU35, Q86UU1, Q8CCJ4, Q8K124, Q8N7J2, Q8TD55, Q96PV7

Diamond homologs: Q5PR69, Q5RG44, Q6NV74, Q6ZU35

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	171
Likely benign	9
Benign	2

Top pathogenic / likely-pathogenic (0)

SpliceAI

2859 predictions. Top by Δscore:

Variant	Effect	Δscore
2:98794672:CTG:C	acceptor_gain	1.0000
2:98794676:T:C	acceptor_gain	1.0000
2:98794676:T:TC	acceptor_gain	1.0000
2:98796114:TCATA:T	donor_loss	1.0000
2:98796115:CATA:C	donor_loss	1.0000
2:98796117:TACCC:T	donor_loss	1.0000
2:98796118:A:AC	donor_gain	1.0000
2:98796118:AC:A	donor_gain	1.0000
2:98796118:ACCC:A	donor_loss	1.0000
2:98796119:C:CC	donor_gain	1.0000
2:98796119:C:CG	donor_loss	1.0000
2:98796119:CC:C	donor_gain	1.0000
2:98796145:T:TA	donor_gain	1.0000
2:98796161:T:TA	donor_gain	1.0000
2:98796262:CTC:C	acceptor_gain	1.0000
2:98796264:CCTGT:C	acceptor_loss	1.0000
2:98797380:T:TA	donor_gain	1.0000
2:98797420:T:TA	donor_gain	1.0000
2:98823534:CGCG:C	acceptor_gain	1.0000
2:98823538:C:CC	acceptor_gain	1.0000
2:98826992:T:C	donor_gain	1.0000
2:98826996:A:AC	donor_gain	1.0000
2:98826997:C:CC	donor_gain	1.0000
2:98826997:CTCGA:C	donor_gain	1.0000
2:98827039:G:C	donor_gain	1.0000
2:98827169:CCT:C	acceptor_loss	1.0000
2:98827173:C:CT	acceptor_gain	1.0000
2:98828589:A:AC	donor_gain	1.0000
2:98828590:C:CC	donor_gain	1.0000
2:98838117:A:AC	donor_gain	1.0000

AlphaMissense

6183 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
2:98794561:A:G	W954R	1.000
2:98794561:A:T	W954R	1.000
2:98794592:C:A	W943C	1.000
2:98794592:C:G	W943C	1.000
2:98794594:A:G	W943R	1.000
2:98794594:A:T	W943R	1.000
2:98794559:C:A	W954C	0.999
2:98794559:C:G	W954C	0.999
2:98794571:T:A	K950N	0.999
2:98794571:T:G	K950N	0.999
2:98794581:G:T	A947D	0.999
2:98794584:A:G	L946P	0.999
2:98832866:A:G	L124P	0.999
2:98832875:A:C	I121S	0.999
2:98832875:A:G	I121T	0.999
2:98832946:G:C	F97L	0.999
2:98832946:G:T	F97L	0.999
2:98832947:A:G	F97S	0.999
2:98832948:A:G	F97L	0.999
2:98832952:A:C	S95R	0.999
2:98832952:A:T	S95R	0.999
2:98832954:T:G	S95R	0.999
2:98832956:T:A	D94V	0.999
2:98794560:C:G	W954S	0.998
2:98794570:A:G	S951P	0.998
2:98794572:T:A	K950I	0.998
2:98794573:T:C	K950E	0.998
2:98794593:C:G	W943S	0.998
2:98827039:G:T	A224D	0.998
2:98832505:A:G	I128T	0.998

dbSNP variants (sampled 300 via entrez): RS1000001146 (2:98912255 G>A), RS1000007486 (2:98926883 T>C), RS1000012168 (2:98843667 T>C), RS1000049631 (2:98892583 C>T), RS1000091601 (2:98824909 C>T), RS1000096215 (2:98882526 G>A), RS1000123827 (2:98850758 C>T), RS1000141994 (2:98854079 C>A,G,T), RS1000161793 (2:98901381 C>A), RS1000179161 (2:98906566 A>C), RS1000186914 (2:98892378 T>C), RS1000230022 (2:98932726 A>C,T), RS1000237181 (2:98803741 T>C), RS1000249438 (2:98818529 G>GCAGACT), RS1000265062 (2:98857794 C>T)

Disease associations

OMIM: gene `` | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

5 associations (top):

Study	Trait	p-value
GCST001241_13	Bipolar disorder	3.000000e-06
GCST008103_118	Bipolar disorder	5.000000e-06
GCST008759_38	Intake of total sugars	8.000000e-07
GCST009205_1	Supramarginal gyrus volume	9.000000e-06
GCST009964_3	Opioid use disorder	2.000000e-07

EFO canonical traits (2, from GWAS)

EFO ID	Trait name
EFO:0010158	sugar consumption measurement
EFO:0010702	opioid use disorder

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

23 total (human), top 23 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
Benzo(a)pyrene	affects methylation, increases expression	3
Aflatoxin B1	decreases expression, decreases methylation, increases methylation	3
sodium arsenite	decreases expression, increases expression	2
Acetaminophen	decreases expression, increases expression	2
Air Pollutants	increases abundance, increases expression	2
Estradiol	affects cotreatment, decreases expression	2
Tobacco Smoke Pollution	decreases expression	2
sodium arsenate	decreases expression, increases abundance	1
sulforaphane	increases expression	1
ferrous chloride	decreases expression	1
S-(1,2-dichlorovinyl)cysteine	affects response to substance, increases expression, affects cotreatment, decreases expression	1
2-palmitoylglycerol	increases expression	1
abrine	decreases expression	1
Arsenic	decreases expression, increases abundance	1
Cisplatin	increases expression	1
Lipopolysaccharides	decreases expression, affects response to substance, increases expression, affects cotreatment	1
Phthalic Acids	decreases methylation	1
Smoke	increases expression, increases abundance	1
Dronabinol	decreases expression	1
Valproic Acid	increases methylation	1
Okadaic Acid	decreases expression	1
beta-Naphthoflavone	decreases expression	1
Particulate Matter	increases abundance, increases expression	1

Clinical trials (associated diseases)

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