SPRYD7

Summary

SPRYD7 (SPRY domain containing 7, HGNC:14297) is a protein-coding gene on chromosome 13q14.2, encoding SPRY domain-containing protein 7 (Q5W111).

At a glance

• GWAS associations: 1
• Clinical variants (ClinVar): 27 total
• MANE Select transcript: NM_020456

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:14297
Approved symbol	SPRYD7
Name	SPRY domain containing 7
Location	13q14.2
Locus type	gene with protein product
Status	Approved
Aliases	CLLD6
Ensembl gene	ENSG00000123178
Ensembl biotype	protein_coding
OMIM	607866
Entrez	57213

Gene structure

Transcript identifiers

Ensembl transcripts: 13 — 12 protein_coding, 1 protein_coding_CDS_not_defined

ENST00000361840, ENST00000378195, ENST00000492258, ENST00000881383, ENST00000881384, ENST00000881385, ENST00000881386, ENST00000881387, ENST00000881388, ENST00000881389, ENST00000917016, ENST00000917017, ENST00000946795

RefSeq mRNA: 2 — MANE Select: NM_020456 NM_001127482, NM_020456

CCDS: CCDS45046, CCDS9422

Canonical transcript exons

ENST00000361840 — 5 exons

Exon	Start	End
ENSE00000682759	49921478	49921580
ENSE00000682761	49927919	49928085
ENSE00001863844	49936130	49936340
ENSE00003480522	49931018	49931134
ENSE00003848508	49912702	49915160

Expression profiles

Bgee: expression breadth ubiquitous, 241 present calls, max score 88.38.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 15.0706 / max 272.7187, expressed in 1790 samples.

FANTOM5 promoters (5 alternative TSS)

Promoter ID	TPM avg	Samples expressed
137333	12.4035	1786
137332	1.7204	1034
137335	0.3924	190
137336	0.3233	107
137334	0.2309	76

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
gastrocnemius	UBERON:0001388	88.38	gold quality
muscle of leg	UBERON:0001383	87.83	gold quality
hindlimb stylopod muscle	UBERON:0004252	87.70	gold quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	85.14	gold quality
dorsolateral prefrontal cortex	UBERON:0009834	84.88	gold quality
Brodmann (1909) area 9	UBERON:0013540	84.84	gold quality
cingulate cortex	UBERON:0003027	84.57	gold quality
anterior cingulate cortex	UBERON:0009835	84.35	gold quality
endothelial cell	CL:0000115	83.95	gold quality
middle temporal gyrus	UBERON:0002771	83.24	gold quality
right frontal lobe	UBERON:0002810	83.24	gold quality
C1 segment of cervical spinal cord	UBERON:0006469	83.16	gold quality
mucosa of transverse colon	UBERON:0004991	82.99	gold quality
muscle organ	UBERON:0001630	82.78	gold quality
amygdala	UBERON:0001876	82.71	gold quality
buccal mucosa cell	CL:0002336	82.63	gold quality
hypothalamus	UBERON:0001898	82.62	gold quality
nucleus accumbens	UBERON:0001882	82.21	gold quality
cortical plate	UBERON:0005343	81.92	gold quality
islet of Langerhans	UBERON:0000006	81.76	gold quality
left adrenal gland	UBERON:0001234	81.48	gold quality
cerebellar hemisphere	UBERON:0002245	81.42	gold quality
caudate nucleus	UBERON:0001873	81.41	gold quality
cerebellar cortex	UBERON:0002129	81.37	gold quality
left adrenal gland cortex	UBERON:0035825	81.27	gold quality
popliteal artery	UBERON:0002250	81.23	gold quality
tibial artery	UBERON:0007610	81.22	gold quality
heart left ventricle	UBERON:0002084	81.12	gold quality
right atrium auricular region	UBERON:0006631	80.97	gold quality
right adrenal gland cortex	UBERON:0035827	80.80	gold quality

Single-cell (SCXA)

Detected in 2 experiment(s), a significant marker in 1.

Experiment	Marker?	Max mean expression
E-ANND-3	yes	8.06
E-HCAD-5	no	2.37

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

122 targeting SPRYD7, 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-1277-5P	100.00	73.95	5056
HSA-MIR-5692A	100.00	74.40	6850
HSA-MIR-6833-3P	100.00	70.63	3197
HSA-MIR-3924	100.00	72.09	2394
HSA-MIR-4476	100.00	68.18	2030
HSA-MIR-6876-5P	100.00	67.68	2126
HSA-MIR-3613-3P	100.00	76.36	7965
HSA-MIR-656-3P	100.00	72.15	2788
HSA-MIR-190A-3P	100.00	80.35	5520
HSA-MIR-4768-5P	100.00	69.49	2861
HSA-MIR-4795-3P	100.00	74.62	4024
HSA-MIR-5011-5P	100.00	83.46	5820
HSA-MIR-513B-5P	99.99	69.96	2150
HSA-MIR-4500	99.99	72.72	2367
HSA-MIR-371B-5P	99.99	75.34	4759
HSA-MIR-186-5P	99.99	70.83	3707
HSA-MIR-4282	99.99	75.36	6408
HSA-MIR-373-5P	99.98	75.36	4753
HSA-MIR-616-5P	99.98	75.58	4775
HSA-MIR-4775	99.98	75.00	6394
HSA-LET-7A-5P	99.98	72.29	1790
HSA-LET-7B-5P	99.98	72.31	1790
HSA-LET-7C-5P	99.98	72.29	1790
HSA-LET-7E-5P	99.98	72.29	1790
HSA-LET-7F-5P	99.98	72.56	1784
HSA-LET-7G-5P	99.98	72.37	1784
HSA-LET-7I-5P	99.98	72.37	1788
HSA-MIR-98-5P	99.98	72.33	1787
HSA-MIR-5696	99.98	72.36	4487
HSA-MIR-520D-5P	99.98	73.34	4883

Literature-anchored findings (GeneRIF, showing 2)

• In the sex-combined analyses, we identified one novel locus (TCF7L2/HABP2) for WHRadjBMI and eight previously established loci at P < 5x10-8: seven for BMI, and one for WHRadjBMI in African ancestry individuals. An additional novel locus (SPRYD7/DLEU2) was identified for WHRadjBMI when combined with European GWAS. (PMID:28430825)
• Functional Proteomics Characterization of the Role of SPRYD7 in Colorectal Cancer Progression and Metastasis. (PMID:37947626)

Cross-species orthologs

6 orthologs

Organism	Symbol	Gene ID
danio_rerio	spryd7a	ENSDARG00000052624
danio_rerio	spryd7b	ENSDARG00000069485
mus_musculus	Spryd7	ENSMUSG00000021930
rattus_norvegicus	Spryd7	ENSRNOG00000015095
drosophila_melanogaster	CG7785	FBGN0038564
caenorhabditis_elegans		WBGENE00008939

Protein

Protein identifiers

SPRY domain-containing protein 7 — Q5W111 (reviewed: Q5W111)

Alternative names: Chronic lymphocytic leukemia deletion region gene 6 protein

All UniProt accessions (2): A0A024RDT6, Q5W111

UniProt curated annotations — full annotation on UniProt →

Isoforms (2)

UniProt ID	Names	Canonical?
Q5W111-1	1	yes
Q5W111-2	2

RefSeq proteins (2): NP_001120954, NP_065189* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR001870	B30.2/SPRY	Domain
IPR003877	SPRY_dom	Domain
IPR013320	ConA-like_dom_sf	Homologous_superfamily
IPR035766	SPRYD7	Family
IPR043136	B30.2/SPRY_sf	Homologous_superfamily

Pfam: PF00622

UniProt features (19 total): strand 12, initiator methionine 1, chain 1, domain 1, modified residue 1, splice variant 1, sequence conflict 1, turn 1

Structure

Experimental structures (PDB)

1 structures.

PDB	Method	Resolution (Å)
7CCB	X-RAY DIFFRACTION	1.62

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q5W111-F1	90.27	0.81

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 (1): 2

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 132 (showing top): YAGI_AML_WITH_INV_16_TRANSLOCATION, BROWNE_HCMV_INFECTION_48HR_DN, RICKMAN_METASTASIS_DN, WANG_LMO4_TARGETS_DN, SCHAEFFER_PROSTATE_DEVELOPMENT_6HR_UP, AAAGGGA_MIR204_MIR211, CHIANG_LIVER_CANCER_SUBCLASS_CTNNB1_UP, chr13q14, NUYTTEN_NIPP1_TARGETS_DN, BRUINS_UVC_RESPONSE_VIA_TP53_GROUP_A, LEE_BMP2_TARGETS_DN, PGF_UP.V1_UP, CHAMP1_TARGET_GENES, ID2_TARGET_GENES, SNIP1_TARGET_GENES

GO Biological Process (0):

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

GO Cellular Component (0):

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
binding	1

Protein interactions and networks

STRING

484 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
SPRYD7	KCNRG	Q8N5I3	675
SPRYD7	CCDC122	Q5T0U0	631
SPRYD7	LACC1	Q8IV20	631
SPRYD7	TRIM13	O60858	617
SPRYD7	SLC41A3	Q96GZ6	600
SPRYD7	NHERF4	Q86UT5	565
SPRYD7	VIL1	P09327	545
SPRYD7	RCBTB1	Q8NDN9	511
SPRYD7	EBPL	Q9BY08	505
SPRYD7	TNP1	P09430	497
SPRYD7	LTA4H	P09960	495
SPRYD7	TNFSF15	O95150	490
SPRYD7	HSDL1	Q3SXM5	472
SPRYD7	ABITRAM	Q9NX38	459
SPRYD7	DLEU7	Q6UYE1	448

IntAct

31 interactions, top by confidence:

A	B	Type	Score
VAC14	SPRYD7	psi-mi:“MI:0915”(physical association)	0.670
SPRYD7	VAC14	psi-mi:“MI:0915”(physical association)	0.670
SPRYD7	CAMK2B	psi-mi:“MI:0915”(physical association)	0.560
TRIP13	SPRYD7	psi-mi:“MI:0915”(physical association)	0.560
NHERF4	SPRYD7	psi-mi:“MI:0915”(physical association)	0.560
CAMK2B	SPRYD7	psi-mi:“MI:0915”(physical association)	0.560
SPRYD7	NHERF4	psi-mi:“MI:0915”(physical association)	0.560
SPRYD7	TRIP13	psi-mi:“MI:0915”(physical association)	0.560
ATP6V0A2	B4GALT3	psi-mi:“MI:0914”(association)	0.530
NYX	LYPLA2	psi-mi:“MI:0914”(association)	0.530
GPC1	SNAP23	psi-mi:“MI:0915”(physical association)	0.400
GPC1	GANAB	psi-mi:“MI:0915”(physical association)	0.400
HAUS7	GOLIM4	psi-mi:“MI:0914”(association)	0.350
SLC37A3	CYB5R3	psi-mi:“MI:0914”(association)	0.350
MAGEA8	METTL15	psi-mi:“MI:0914”(association)	0.350
SPAG6	MT-ND1	psi-mi:“MI:0914”(association)	0.350
SLC37A3	APOB	psi-mi:“MI:0914”(association)	0.350
SPRYD7	HARS2	psi-mi:“MI:0914”(association)	0.350
LRRC73	SLC27A2	psi-mi:“MI:0914”(association)	0.350
HAUS7	SLC27A2	psi-mi:“MI:0914”(association)	0.350
SPRYD7	SLC25A12	psi-mi:“MI:0914”(association)	0.350
HAUS7	RFPL4A	psi-mi:“MI:0914”(association)	0.350
UBASH3A	SPRYD7	psi-mi:“MI:0915”(physical association)	0.000

BioGRID (54): SPRYD7 (Two-hybrid), SPRYD7 (Two-hybrid), SPRYD7 (Two-hybrid), PDZD3 (Two-hybrid), SPRYD7 (Affinity Capture-MS), SPRYD7 (Affinity Capture-MS), SPRYD7 (Affinity Capture-MS), SPRYD7 (Affinity Capture-MS), SPRYD7 (Affinity Capture-MS), SPRYD7 (Affinity Capture-MS), SPRYD7 (Affinity Capture-RNA), SPRYD7 (Two-hybrid), SPRYD7 (Two-hybrid), SPRYD7 (Two-hybrid), SPRYD7 (Two-hybrid)

ESM2 similar proteins: A1Z6E0, A6QLT2, A8QGZ7, B0X9V1, B3MDR0, B3NRP1, B4F739, B4GBN7, B4HQ29, B4J6Q0, B4KNC5, B4LMQ3, B4MR59, B4P4K8, B4QE02, P0C2W1, P0CH38, P11029, P11497, P23727, P26450, P27986, P28173, P35433, P47196, P53041, P53042, Q06203, Q13614, Q16XV7, Q290L5, Q2T9X3, Q3TFQ1, Q5E9X6, Q5M7T2, Q5R685, Q5REB9, Q5SWU9, Q5W111, Q5ZIV1

Diamond homologs: Q2T9X3, Q3TFQ1, Q5M7T2, Q5W111, Q5ZHV7

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	18
Likely benign	0
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

1320 predictions. Top by Δscore:

Variant	Effect	Δscore
13:49921472:GCTT:G	donor_loss	1.0000
13:49921473:CTTA:C	donor_loss	1.0000
13:49921474:TTAC:T	donor_loss	1.0000
13:49921475:TA:T	donor_loss	1.0000
13:49921476:A:AC	donor_gain	1.0000
13:49921476:ACCA:A	donor_loss	1.0000
13:49921477:C:CA	donor_loss	1.0000
13:49921477:C:CC	donor_gain	1.0000
13:49921577:TACC:T	acceptor_gain	1.0000
13:49921579:CC:C	acceptor_gain	1.0000
13:49921580:CC:C	acceptor_gain	1.0000
13:49921581:C:CC	acceptor_gain	1.0000
13:49927932:T:TA	donor_gain	1.0000
13:49936124:CCTTA:C	donor_loss	1.0000
13:49936125:CTTA:C	donor_loss	1.0000
13:49936126:TTAC:T	donor_loss	1.0000
13:49936127:TACC:T	donor_loss	1.0000
13:49936128:A:AC	donor_gain	1.0000
13:49936128:AC:A	donor_gain	1.0000
13:49936129:C:A	donor_loss	1.0000
13:49936129:C:CC	donor_gain	1.0000
13:49936129:CC:C	donor_gain	1.0000
13:49921576:ATACC:A	acceptor_gain	0.9900
13:49921578:ACCCT:A	acceptor_loss	0.9900
13:49921579:CCCTA:C	acceptor_loss	0.9900
13:49921580:CCTAG:C	acceptor_loss	0.9900
13:49921581:C:T	acceptor_gain	0.9900
13:49921581:CTAG:C	acceptor_loss	0.9900
13:49921582:T:G	acceptor_loss	0.9900
13:49927911:GAACT:G	donor_loss	0.9900

AlphaMissense

1295 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
13:49928080:A:G	W77R	1.000
13:49928080:A:T	W77R	1.000
13:49931086:C:T	G52E	1.000
13:49931092:C:T	G50E	1.000
13:49931122:A:T	V40D	1.000
13:49915088:A:C	I189R	0.999
13:49915088:A:T	I189K	0.999
13:49915096:A:C	F186L	0.999
13:49915096:A:T	F186L	0.999
13:49915098:A:G	F186L	0.999
13:49915145:A:T	I170N	0.999
13:49915148:G:T	A169E	0.999
13:49915149:C:G	A169P	0.999
13:49921483:A:T	V163D	0.999
13:49921489:G:C	P161R	0.999
13:49921489:G:T	P161Q	0.999
13:49921565:G:C	H136D	0.999
13:49921571:A:C	Y134D	0.999
13:49928012:A:C	S99R	0.999
13:49928012:A:T	S99R	0.999
13:49928014:T:G	S99R	0.999
13:49928064:G:T	A82E	0.999
13:49928065:C:G	A82P	0.999
13:49928067:A:T	V81D	0.999
13:49928070:C:T	G80D	0.999
13:49928071:C:G	G80R	0.999
13:49928077:C:G	G78R	0.999
13:49928085:C:T	G75E	0.999
13:49931045:A:C	Y66D	0.999
13:49931046:G:C	S65R	0.999

dbSNP variants (sampled 300 via entrez): RS1000162391 (13:49928017 G>A,T), RS1000278009 (13:49918519 C>T), RS1000363571 (13:49936528 T>A,C), RS1000470058 (13:49927490 T>A,C), RS1000588049 (13:49936707 C>T), RS1000605414 (13:49922076 T>C), RS1000766378 (13:49935079 C>T), RS1000878383 (13:49917022 T>C,G), RS1000992158 (13:49915404 C>T), RS1001169477 (13:49926021 G>A), RS1001272043 (13:49919383 A>C), RS1001323115 (13:49923888 C>G,T), RS1001373517 (13:49933371 C>T), RS1001375585 (13:49918157 G>A), RS1001415784 (13:49922478 C>T)

Disease associations

OMIM: gene MIM:607866 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

1 associations (top):

Study	Trait	p-value
GCST004518_1	Waist-to-hip ratio adjusted for body mass index	4.000000e-08

EFO canonical traits (1, from GWAS)

EFO ID	Trait name
EFO:0007788	BMI-adjusted waist-hip ratio

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

29 total (human), top 29 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
Valproic Acid	affects expression, affects cotreatment, increases expression	7
aristolochic acid I	decreases expression	1
methylmercuric chloride	decreases expression	1
triphenyl phosphate	affects expression	1
bisphenol A	increases expression	1
lead acetate	increases expression	1
sodium arsenite	affects expression	1
2-bromopalmitate	decreases reaction, increases abundance, increases palmitoylation	1
4-aminophenylarsenoxide	affects binding, decreases reaction	1
di-n-butylphosphoric acid	affects expression	1
entinostat	increases expression	1
4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamide	affects cotreatment, increases expression	1
dorsomorphin	affects cotreatment, increases expression	1
Arsenic Trioxide	affects binding, decreases reaction	1
Acetaminophen	decreases expression	1
Benzo(a)pyrene	increases expression	1
Cadmium	increases palmitoylation, decreases reaction, increases abundance	1
Diethylstilbestrol	decreases expression	1
Doxorubicin	decreases expression	1
Estradiol	increases expression	1
Ethyl Methanesulfonate	increases expression	1
Ivermectin	decreases expression	1
Lead	affects expression	1
Methyl Methanesulfonate	increases expression	1
Tobacco Smoke Pollution	increases expression	1
Tretinoin	decreases expression	1
Cadmium Chloride	increases abundance, increases palmitoylation, decreases reaction	1
Copper Sulfate	decreases expression	1
Lactic Acid	decreases expression	1

Clinical trials (associated diseases)

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