SCARF2

Summary

SCARF2 (scavenger receptor class F member 2, HGNC:19869) is a protein-coding gene on chromosome 22q11.21, encoding Scavenger receptor class F member 2 (Q96GP6). Probable adhesion protein, which mediates homophilic and heterophilic interactions.

The protein encoded by this gene is similar to SCARF1/SREC-I, a scavenger receptor protein that mediates the binding and degradation of acetylated low density lipoprotein (Ac-LDL). This protein has only little activity of internalizing modified low density lipoproteins (LDL), but it can interact with SCARF1 through its extracellular domain. The association of this protein with SCARF1 is suppressed by the presence of scavenger ligands. Alternatively spliced transcript variants encoding distinct isoforms have been reported.

Source: NCBI Gene 91179 — RefSeq curated summary.

At a glance

• Gene–disease (curated): van den Ende-Gupta syndrome (Definitive, GenCC)
• GWAS associations: 4
• Clinical variants (ClinVar): 287 total — 8 pathogenic, 7 likely-pathogenic
• Phenotypes (HPO): 79
• Dosage sensitivity (ClinGen): haploinsufficiency autosomal recessive, triplosensitivity no evidence
• MANE Select transcript: NM_182895

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:19869
Approved symbol	SCARF2
Name	scavenger receptor class F member 2
Location	22q11.21
Locus type	gene with protein product
Status	Approved
Aliases	SREC-II, SREC2, HUMZD58C02
Ensembl gene	ENSG00000244486
Ensembl biotype	protein_coding
OMIM	613619
Entrez	91179

Gene structure

Transcript identifiers

Ensembl transcripts: 12 — 11 protein_coding, 1 retained_intron

ENST00000494535, ENST00000622235, ENST00000623402, ENST00000925309, ENST00000925310, ENST00000925311, ENST00000925312, ENST00000925313, ENST00000925314, ENST00000925315, ENST00000967704, ENST00000967705

RefSeq mRNA: 2 — MANE Select: NM_182895 NM_153334, NM_182895

CCDS: CCDS13779, CCDS46666

Canonical transcript exons

ENST00000622235 — 11 exons

Exon	Start	End
ENSE00000000098	20424584	20426282
ENSE00003717000	20429730	20429833
ENSE00003718979	20431018	20431537
ENSE00003720074	20431745	20431846
ENSE00003727687	20427398	20427550
ENSE00003731878	20431930	20431988
ENSE00003736721	20437582	20437825
ENSE00003738259	20430690	20430908
ENSE00003740217	20429536	20429653
ENSE00003744167	20429225	20429340
ENSE00003749346	20430429	20430557

Expression profiles

Bgee: expression breadth ubiquitous, 165 present calls, max score 92.97.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 13.3754 / max 181.9601, expressed in 1202 samples.

FANTOM5 promoters (5 alternative TSS)

Promoter ID	TPM avg	Samples expressed
193199	12.7134	1186
209397	0.5030	340
193195	0.0789	21
193196	0.0605	22
193198	0.0196	5

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
right coronary artery	UBERON:0001625	92.97	gold quality
ascending aorta	UBERON:0001496	92.70	gold quality
stromal cell of endometrium	CL:0002255	92.53	gold quality
thoracic aorta	UBERON:0001515	92.53	gold quality
aorta	UBERON:0000947	91.79	gold quality
mucosa of stomach	UBERON:0001199	91.65	gold quality
tibial artery	UBERON:0007610	91.59	gold quality
popliteal artery	UBERON:0002250	91.58	gold quality
left coronary artery	UBERON:0001626	90.44	gold quality
descending thoracic aorta	UBERON:0002345	90.28	gold quality
coronary artery	UBERON:0001621	88.91	gold quality
right lung	UBERON:0002167	87.93	gold quality
endocervix	UBERON:0000458	87.45	gold quality
tibial nerve	UBERON:0001323	86.99	gold quality
right ovary	UBERON:0002118	86.37	gold quality
right uterine tube	UBERON:0001302	86.28	gold quality
left ovary	UBERON:0002119	86.21	gold quality
body of uterus	UBERON:0009853	85.77	gold quality
upper lobe of left lung	UBERON:0008952	85.46	gold quality
esophagogastric junction muscularis propria	UBERON:0035841	84.98	gold quality
ectocervix	UBERON:0012249	84.73	gold quality
left uterine tube	UBERON:0001303	84.48	gold quality
upper lobe of lung	UBERON:0008948	84.30	gold quality
metanephros cortex	UBERON:0010533	83.68	gold quality
omental fat pad	UBERON:0010414	83.13	gold quality
peritoneum	UBERON:0002358	83.05	gold quality
lower esophagus muscularis layer	UBERON:0035833	82.21	gold quality
lower esophagus	UBERON:0013473	82.14	gold quality
adipose tissue of abdominal region	UBERON:0007808	81.48	gold quality
left lobe of thyroid gland	UBERON:0001120	81.26	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	yes	3.39
E-GEOD-124858	no	8.75

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

25 targeting SCARF2, 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-10401-5P	99.99	65.79	948
HSA-MIR-6780A-5P	99.88	66.69	2776
HSA-MIR-3151-5P	99.86	63.83	1069
HSA-MIR-4728-5P	99.85	69.39	4718
HSA-MIR-6785-5P	99.82	68.68	4428
HSA-MIR-1273H-5P	99.77	66.32	2471
HSA-MIR-149-3P	99.72	68.22	3963
HSA-MIR-30B-3P	99.70	65.76	2325
HSA-MIR-3689A-3P	99.70	65.73	2306
HSA-MIR-3689B-3P	99.70	65.71	2311
HSA-MIR-3689C	99.70	65.71	2311
HSA-MIR-6779-5P	99.70	65.76	2363
HSA-MIR-6883-5P	99.69	68.05	3785
HSA-MIR-3202	99.66	67.70	2737
HSA-MIR-7106-5P	99.53	67.47	3574
HSA-MIR-92B-5P	99.36	63.29	110
HSA-MIR-6799-5P	99.14	65.72	2093
HSA-MIR-7160-5P	99.11	67.17	2207
HSA-MIR-548S	98.50	67.17	1213
HSA-MIR-1972	97.67	67.38	1172
HSA-MIR-3187-3P	97.38	65.80	904
HSA-MIR-4701-5P	96.45	68.41	1121
HSA-MIR-588	96.45	68.36	1127
HSA-MIR-4435	95.90	65.47	1201
HSA-MIR-6853-5P	93.94	61.88	114

Functional genomics

ClinGen dosage: haploinsufficiency 30 (autosomal recessive), triplosensitivity 0 (no evidence). ClinGen Gene Dosage Map

Literature-anchored findings (GeneRIF, showing 5)

• SRECII binds to SRECI and has a similar tissue distribution pattern (PMID:12154095)
• Mutations in SCARF2 are responsible for Van Den Ende-Gupta syndrome. (PMID:20887961)
• the full VDEGS phenotype may include sclerocornea resulting from homozygosity or compound heterozygosity for loss of function variants in SCARF2. (PMID:24478002)
• Further delineation of van den Ende-Gupta syndrome: Genetic heterogeneity and overlap with congenital heart defects and skeletal malformations syndrome. (PMID:33783941)
• Two novel variants in SCARF2 gene underlie van den Ende-Gupta syndrome. (PMID:35224863)

Cross-species orthologs

3 orthologs

Organism	Symbol	Gene ID
danio_rerio	SCARF2	ENSDARG00000114825
mus_musculus	Scarf2	ENSMUSG00000012017
rattus_norvegicus	Scarf2	ENSRNOG00000000288

Paralogs (3): SCARF1 (ENSG00000074660), CRB3 (ENSG00000130545), CRB2 (ENSG00000148204)

Protein

Protein identifiers

Scavenger receptor class F member 2 — Q96GP6 (reviewed: Q96GP6)

Alternative names: SRECRP-1, Scavenger receptor expressed by endothelial cells 2 protein

All UniProt accessions (1): Q96GP6

UniProt curated annotations — full annotation on UniProt →

Function. Probable adhesion protein, which mediates homophilic and heterophilic interactions. In contrast to SCARF1, it poorly mediates the binding and degradation of acetylated low density lipoprotein (Ac-LDL).

Subunit / interactions. Homophilic and heterophilic interaction via its extracellular domain. Interacts with SCARF1. The heterophilic interaction with SCARF1, which is stronger than the homophilic interaction with itself, is suppressed by the presence of SCARF1 ligand such as Ac-LDL.

Subcellular location. Membrane.

Tissue specificity. Predominantly expressed in endothelial cells. Expressed in heart, placenta, lung, kidney, spleen, small intestine and ovary.

Disease relevance. Van den Ende-Gupta syndrome (VDEGS) [MIM:600920] A syndrome characterized by craniofacial and skeletal abnormalities that include blepharophimosis, a flat and wide nasal bridge, narrow and beaked nose, hypoplastic maxilla with or without cleft palate and everted lower lip, prominent ears, down-slanting eyes, arachnodactyly, and camptodactyly. Patients present congenital joint contractures that improve without intervention, and normal growth and development. Intelligence is normal. Rarely, enlarged cerebella can be present. Some patients experience respiratory problems due to laryngeal abnormalities. The disease is caused by variants affecting the gene represented in this entry.

Isoforms (2)

UniProt ID	Names	Canonical?
Q96GP6-1	1	yes
Q96GP6-2	2

RefSeq proteins (2): NP_699165, NP_878315* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR000742	EGF	Domain
IPR002049	LE_dom	Domain
IPR009030	Growth_fac_rcpt_cys_sf	Homologous_superfamily
IPR042635	MEGF10/SREC1/2-like	Family

UniProt features (64 total): disulfide bond 21, sequence variant 9, modified residue 8, domain 7, compositionally biased region 6, glycosylation site 4, region of interest 2, topological domain 2, signal peptide 1, chain 1, transmembrane region 1, splice variant 1, sequence conflict 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q96GP6-F1	64.63	0.26

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 (8): 551, 613, 628, 651, 653, 710, 718, 742

Disulfide bonds (21): 75–86, 80–98, 100–109, 126–134, 128–141, 143–152, 156–163, 158–170, 172–181, 185–193, 187–200, 202–211, 215–222, 217–229, 231–240, 244–251, 246–258, 260–269, 376–384, 379–391 …

Glycosylation sites (4): 83, 310, 365, 403

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 253 (showing top): GOBP_HETEROPHILIC_CELL_CELL_ADHESION, GOBP_VESICLE_MEDIATED_TRANSPORT, GGGTGGRR_PAX4_03, SP1_Q2_01, GOBP_CELL_CELL_ADHESION, NKX22_01, WGGAATGY_TEF1_Q6, GOCC_ANCHORING_JUNCTION, GOMF_SCAVENGER_RECEPTOR_ACTIVITY, GOMF_CARGO_RECEPTOR_ACTIVITY, PIONTEK_PKD1_TARGETS_DN, MEISSNER_NPC_HCP_WITH_H3_UNMETHYLATED, MEISSNER_BRAIN_HCP_WITH_H3K27ME3, TAL1BETAITF2_01, HATADA_METHYLATED_IN_LUNG_CANCER_UP

GO Biological Process (3): heterophilic cell-cell adhesion (GO:0007157), cell adhesion (GO:0007155), vesicle-mediated transport (GO:0016192)

GO Molecular Function (2): scavenger receptor activity (GO:0005044), protein binding (GO:0005515)

GO Cellular Component (2): focal adhesion (GO:0005925), membrane (GO:0016020)

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
cellular process	2
cell-cell adhesion	1
transport	1
cargo receptor activity	1
binding	1
cell-substrate junction	1
cellular anatomical structure	1

Protein interactions and networks

STRING

696 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
SCARF2	ZNF74	Q16587	583
SCARF2	A0A590UK56	A0A590UK56	491
SCARF2	TGM3	Q08188	490
SCARF2	EGF	P01133	487
SCARF2	KLHL22	Q53GT1	480
SCARF2	SPATA6	Q9NWH7	479
SCARF2	AIFM3	Q96NN9	453
SCARF2	SNAP29	O95721	448
SCARF2	LZTR1	Q8N653	447
SCARF2	TANGO2	Q6ICL3	445
SCARF2	CALML5	Q9NZT1	435
SCARF2	THAP7	Q9BT49	419
SCARF2	PI4KA	P42356	404
SCARF2	GP1BB	P13224	404
SCARF2	LRRC74B	Q6ZQY2	398

IntAct

33 interactions, top by confidence:

A	B	Type	Score
CFTR	ESYT2	psi-mi:“MI:2364”(proximity)	0.710
KLHL22	TMEM223	psi-mi:“MI:0914”(association)	0.640
SCARF2	FYN	psi-mi:“MI:0915”(physical association)	0.560
SLC39A5	TMEM223	psi-mi:“MI:0914”(association)	0.530
SPINT2	UPK3BL1	psi-mi:“MI:0914”(association)	0.530
TNFRSF13B	TNFRSF10B	psi-mi:“MI:0914”(association)	0.530
ANKH	FAM234B	psi-mi:“MI:0914”(association)	0.530
ABL1	SCARF2	psi-mi:“MI:0915”(physical association)	0.400
SCARF2	GRB2	psi-mi:“MI:0915”(physical association)	0.400
SCARF2	NCK1	psi-mi:“MI:0915”(physical association)	0.400
SFTPC	CBX6	psi-mi:“MI:0914”(association)	0.350
LDLRAD1	GXYLT2	psi-mi:“MI:0914”(association)	0.350
NOTCH2	ZNF320	psi-mi:“MI:0914”(association)	0.350
CHRNB2	TMEM131L	psi-mi:“MI:0914”(association)	0.350
SAAL1	QSOX1	psi-mi:“MI:0914”(association)	0.350
SFTPC	MPZL1	psi-mi:“MI:0914”(association)	0.350
ITGB2	CD151	psi-mi:“MI:0914”(association)	0.350
CCNI2	ZNF609	psi-mi:“MI:0914”(association)	0.350
CLGN	TMEM131L	psi-mi:“MI:0914”(association)	0.350
FYN	MYCBP2	psi-mi:“MI:0914”(association)	0.350
P4HA3	ARHGAP10	psi-mi:“MI:0914”(association)	0.350
S1PR4	ECD	psi-mi:“MI:0914”(association)	0.350
SH3KBP1	ARHGAP10	psi-mi:“MI:0914”(association)	0.350
TMEM74	MGAM	psi-mi:“MI:0914”(association)	0.350
SLC15A3	GXYLT2	psi-mi:“MI:0914”(association)	0.350
SLC39A10	CASK	psi-mi:“MI:0914”(association)	0.350

BioGRID (49): SCARF2 (Affinity Capture-MS), SCARF2 (Affinity Capture-MS), SCARF2 (Affinity Capture-MS), SCARF2 (Affinity Capture-MS), SCARF2 (Proximity Label-MS), SCARF2 (Affinity Capture-MS), SCARF2 (Proximity Label-MS), SCARF2 (Affinity Capture-MS), SCARF2 (Affinity Capture-MS), SCARF2 (Affinity Capture-MS), SCARF2 (Affinity Capture-MS), SCARF2 (Affinity Capture-MS), SCARF2 (Affinity Capture-MS), SCARF2 (Affinity Capture-MS), SCARF2 (Affinity Capture-MS)

ESM2 similar proteins: A1L0T3, A1L4H1, A6QNY1, D3YZF7, O95428, P28698, P30203, P55068, P55106, P59222, P98162, Q04756, Q14767, Q28019, Q28062, Q28256, Q28343, Q28670, Q3U515, Q4G0T1, Q5F378, Q5HZW5, Q61003, Q61361, Q6H9L7, Q6KF10, Q6PGE4, Q6QNF4, Q7TQH7, Q7Z4F1, Q86T13, Q86VR7, Q86VZ4, Q8BV57, Q8BZE1, Q8CB67, Q8VCP9, Q8WTU2, Q91V98, Q96DN2

Diamond homologs: P59222, Q14162, Q5ND28, Q6AZ60, Q96GP6, Q9QXT5, Q14766, Q8CG19, A0JM12, A6BM72, E9QJQ6, Q6DIB5, Q80T91, Q96KG7

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	8
Likely pathogenic	7
Uncertain significance	167
Likely benign	45
Benign	45

Top pathogenic / likely-pathogenic (15)

Variant ID	HGVS	Classification
1184854	NM_182895.5(SCARF2):c.651C>G (p.Cys217Trp)	Pathogenic
1184855	NM_182895.5(SCARF2):c.466TGCCAG[1] (p.156CQ[1])	Pathogenic
144050	NM_182895.5(SCARF2):c.190T>C (p.Cys64Arg)	Pathogenic
144051	NM_182895.5(SCARF2):c.2531del (p.Gln844fs)	Pathogenic
1526095	NM_182895.5(SCARF2):c.1104C>A (p.Tyr368Ter)	Pathogenic
1697232	NM_182895.5(SCARF2):c.220G>T (p.Glu74Ter)	Pathogenic
190239	NM_182895.5(SCARF2):c.441_457del (p.Trp148fs)	Pathogenic
31047	NM_182895.5(SCARF2):c.1328_1329del (p.Val443fs)	Pathogenic
191319	Single allele	Likely pathogenic
2500262	NM_182895.5(SCARF2):c.3G>A (p.Met1Ile)	Likely pathogenic
31046	NM_182895.5(SCARF2):c.773G>A (p.Cys258Tyr)	Likely pathogenic
4533365	NM_182895.5(SCARF2):c.15del (p.Arg7fs)	Likely pathogenic
4845895	NM_182895.5(SCARF2):c.2227_2238delinsAGGCGGGGCCGCA (p.Ala743fs)	Likely pathogenic
803645	NM_182895.5(SCARF2):c.915C>G (p.Cys305Trp)	Likely pathogenic
993021	NM_182895.5(SCARF2):c.25del (p.Ala9fs)	Likely pathogenic

SpliceAI

1665 predictions. Top by Δscore:

Variant	Effect	Δscore
22:20427551:C:CC	acceptor_gain	1.0000
22:20429228:CGA:C	donor_gain	1.0000
22:20429649:GGTTT:G	acceptor_gain	1.0000
22:20429650:GTTT:G	acceptor_gain	1.0000
22:20429651:TTT:T	acceptor_gain	1.0000
22:20429651:TTTC:T	acceptor_loss	1.0000
22:20429652:TT:T	acceptor_gain	1.0000
22:20429653:TC:T	acceptor_loss	1.0000
22:20429654:C:CA	acceptor_loss	1.0000
22:20429654:C:CC	acceptor_gain	1.0000
22:20429725:CTTA:C	donor_loss	1.0000
22:20429726:TTA:T	donor_loss	1.0000
22:20429726:TTAC:T	donor_loss	1.0000
22:20429727:TA:T	donor_loss	1.0000
22:20429728:A:AC	donor_gain	1.0000
22:20429728:A:T	donor_loss	1.0000
22:20429729:C:CC	donor_gain	1.0000
22:20429729:C:CG	donor_loss	1.0000
22:20429829:TACAG:T	acceptor_gain	1.0000
22:20429830:ACAG:A	acceptor_gain	1.0000
22:20429831:CAG:C	acceptor_gain	1.0000
22:20429831:CAGC:C	acceptor_gain	1.0000
22:20429832:AG:A	acceptor_gain	1.0000
22:20429834:C:CA	acceptor_loss	1.0000
22:20429834:C:CC	acceptor_gain	1.0000
22:20429834:CTGCC:C	acceptor_loss	1.0000
22:20430425:TCACT:T	donor_loss	1.0000
22:20430426:CACTG:C	donor_loss	1.0000
22:20430427:A:AC	donor_gain	1.0000
22:20430427:ACTG:A	donor_loss	1.0000

AlphaMissense

5545 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
22:20430526:C:A	G369C	1.000
22:20430543:C:G	C363S	1.000
22:20430544:A:T	C363S	1.000
22:20430555:C:G	C359S	1.000
22:20430556:A:T	C359S	1.000
22:20430701:C:A	W354C	1.000
22:20430701:C:G	W354C	1.000
22:20430706:C:A	G353C	1.000
22:20430714:C:G	C350S	1.000
22:20430715:A:T	C350S	1.000
22:20430723:C:G	C347S	1.000
22:20430724:A:T	C347S	1.000
22:20430729:C:A	G345V	1.000
22:20430729:C:T	G345D	1.000
22:20430730:C:A	G345C	1.000
22:20430822:C:G	C314S	1.000
22:20430823:A:T	C314S	1.000
22:20430836:C:A	W309C	1.000
22:20430836:C:G	W309C	1.000
22:20430865:C:A	G300C	1.000
22:20430879:C:T	C295Y	1.000
22:20431341:C:A	W177C	1.000
22:20431341:C:G	W177C	1.000
22:20431428:C:A	W148C	1.000
22:20431428:C:G	W148C	1.000
22:20431471:C:G	C134S	1.000
22:20431472:A:T	C134S	1.000
22:20431506:G:C	C122W	1.000
22:20431507:C:A	C122F	1.000
22:20431507:C:G	C122S	1.000

dbSNP variants (sampled 300 via entrez): RS1000070173 (22:20424393 A>G), RS1000795919 (22:20424467 C>A), RS1000867807 (22:20430962 C>A), RS1001077005 (22:20424208 C>G), RS1001078956 (22:20430557 C>T), RS1001164069 (22:20436601 G>A), RS1001362308 (22:20428693 G>T), RS1001427213 (22:20436837 G>T), RS1001492875 (22:20437864 C>A,T), RS1001535525 (22:20434991 T>C), RS1001698881 (22:20432308 G>A), RS1001758969 (22:20426548 C>G,T), RS1001813285 (22:20429045 G>A), RS1001956617 (22:20427970 C>T), RS1002070273 (22:20426730 C>G)

Disease associations

OMIM: gene MIM:613619 | disease phenotypes: MIM:600920

GenCC curated gene-disease

Disease	Classification	Inheritance
van den Ende-Gupta syndrome	Definitive	Autosomal recessive

Mondo (2): van den Ende-Gupta syndrome (MONDO:0010959), microcephaly (MONDO:0001149)

Orphanet (1): Van den Ende-Gupta syndrome (Orphanet:2460)

HPO phenotypes

79 total (30 of 79 shown, HPO-id order):

HPO	Term
HP:0000007	Autosomal recessive inheritance
HP:0000126	Hydronephrosis
HP:0000160	Narrow mouth
HP:0000175	Cleft palate
HP:0000218	High palate
HP:0000232	Everted lower lip vermilion
HP:0000272	Malar flattening
HP:0000324	Facial asymmetry
HP:0000325	Triangular face
HP:0000327	Hypoplasia of the maxilla
HP:0000347	Micrognathia
HP:0000358	Posteriorly rotated ears
HP:0000365	Hearing impairment
HP:0000385	Small earlobe
HP:0000396	Overfolded helix
HP:0000411	Protruding ear
HP:0000430	Underdeveloped nasal alae
HP:0000444	Convex nasal ridge
HP:0000452	Choanal stenosis
HP:0000460	Narrow nose
HP:0000494	Downslanted palpebral fissures
HP:0000534	Abnormal eyebrow morphology
HP:0000581	Blepharophimosis
HP:0000647	Sclerocornea
HP:0000678	Dental crowding
HP:0000750	Delayed speech and language development
HP:0000767	Pectus excavatum
HP:0000773	Short ribs
HP:0000882	Hypoplastic scapulae
HP:0000883	Thin ribs

GWAS associations

4 associations (top):

Study	Trait	p-value
GCST007430_11	Peak expiratory flow	7.000000e-07
GCST007431_78	Lung function (FEV1/FVC)	3.000000e-19
GCST007432_205	FEV1	7.000000e-11
GCST90000025_703	Appendicular lean mass	5.000000e-19

EFO canonical traits (4, from GWAS)

EFO ID	Trait name
EFO:0009718	peak expiratory flow
EFO:0004713	FEV/FVC ratio
EFO:0004314	forced expiratory volume
EFO:0004980	appendicular lean mass

MeSH disease descriptors (2)

Descriptor	Name	Tree numbers
D008831	Microcephaly	C05.660.207.620; C10.500.507.400.500; C16.131.621.207.620; C16.131.666.507.400.500
C535909	Marden Walker like syndrome (supp.)

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

32 total (human), top 30 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
Arsenic	affects cotreatment, increases abundance, increases expression, affects methylation	2
Benzo(a)pyrene	decreases expression, increases methylation	2
Tobacco Smoke Pollution	decreases expression, increases methylation	2
aristolochic acid I	increases expression	1
FR900359	affects phosphorylation	1
triphenyl phosphate	affects expression	1
lead acetate	decreases expression	1
potassium perchlorate	decreases expression	1
tris(2-butoxyethyl) phosphate	affects expression	1
beta-lapachone	increases expression	1
sodium arsenite	affects cotreatment, increases abundance, increases expression	1
butyraldehyde	decreases expression	1
manganese chloride	affects cotreatment, increases abundance, increases expression	1
vanadyl sulfate	decreases expression	1
beta-methylcholine	affects expression	1
perfluorooctane sulfonic acid	increases expression	1
Sunitinib	decreases expression	1
Arsenic Trioxide	decreases expression	1
Air Pollutants	decreases expression, increases abundance	1
Allergens	decreases expression	1
Calcitriol	decreases expression	1
Copper	increases expression, affects binding	1
Disulfiram	affects binding, increases expression	1
Estradiol	affects cotreatment, increases expression	1
Manganese	affects cotreatment, increases abundance, increases expression	1
Urethane	increases expression	1
Valproic Acid	increases methylation	1
Aflatoxin B1	decreases expression	1
Okadaic Acid	decreases expression	1
Acrylamide	increases expression	1

Clinical trials (associated diseases)

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

Trial	Phase	Status	Title
NCT05518188	PHASE1/PHASE2	RECRUITING	Melpida: Recombinant Adeno-associated Virus (serotype 9) Encoding a Codon Optimized Human AP4M1 Transgene (hAP4M1opt)
NCT00001639	Not specified	COMPLETED	Evaluation of Patients With Unresolved Chromosome Abnormalities
NCT01151462	Not specified	WITHDRAWN	Postnatal HCMV Infection in Very Preterm Infants. Implications, Morbidity, Growth and Neurodevelopmental Outcomes.
NCT01565005	Not specified	COMPLETED	Microcephaly Genetic Deficiency in Neural Progenitors
NCT02510170	Not specified	COMPLETED	Fetal and Maternal Head Circumference During Pregnancy in Israeli Population
NCT02741882	Not specified	COMPLETED	Zika and Microcephaly: Case-control Study
NCT02943304	Not specified	COMPLETED	Neurodevelopment Outcome of Newborns Exposed to Zika Virus (ZIKV) in Utero
NCT03255369	Not specified	UNKNOWN	Vertical Exposure to Zika Virus and Its Consequences for Child Neurodevelopment (ZIKVIRUSIFF)
NCT03325946	Not specified	RECRUITING	The FBRI VTC Neuromotor Research Clinic
NCT03330600	Not specified	COMPLETED	Efficacy of Aquatic Physiotherapy in Children With Microcephaly by Zika Virus Congenital Syndrome
NCT03548779	Not specified	COMPLETED	North Carolina Genomic Evaluation by Next-generation Exome Sequencing, 2
NCT03651687	Not specified	COMPLETED	Guangzhou Surveillance and Clinical Study in Microcephaly (GSCSM)
NCT03922594	Not specified	TERMINATED	Surveillance of Zika-related Microcephaly in Sub-Saharan Africa and Asia
NCT04816175	Not specified	COMPLETED	Intensive Therapy for Children With Microcephaly, Hyperkinetic Movements, or Global Developmental Delay
NCT05322980	Not specified	COMPLETED	Summary of Infants Weighing 500 Grams or Less
NCT06019182	Not specified	RECRUITING	MEHMO Natural History and Biomarkers
NCT06566066	Not specified	RECRUITING	Register for Patients With Thyroid Hormone Resistance.