SIRPD

Summary

SIRPD (signal regulatory protein delta, HGNC:16248) is a protein-coding gene on chromosome 20p13, encoding Signal-regulatory protein delta (Q9H106).

Predicted to be located in extracellular region. Predicted to be active in plasma membrane.

Source: NCBI Gene 128646 — RefSeq curated summary.

At a glance

• GWAS associations: 4
• Clinical variants (ClinVar): 32 total
• MANE Select transcript: NM_178460

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:16248
Approved symbol	SIRPD
Name	signal regulatory protein delta
Location	20p13
Locus type	gene with protein product
Status	Approved
Aliases	dJ576H24.4
Ensembl gene	ENSG00000125900
Ensembl biotype	protein_coding
OMIM	621320
Entrez	128646

Gene structure

Transcript identifiers

Ensembl transcripts: 3 — 3 protein_coding

ENST00000381621, ENST00000381623, ENST00000429387

RefSeq mRNA: 2 — MANE Select: NM_178460 NM_001410802, NM_178460

CCDS: CCDS13018, CCDS93001

Canonical transcript exons

ENST00000381623 — 4 exons

Exon	Start	End
ENSE00000906696	1537155	1537310
ENSE00001489267	1557581	1557705
ENSE00001489271	1534251	1534441
ENSE00003474067	1551691	1552038

Expression profiles

Bgee: expression breadth ubiquitous, 122 present calls, max score 96.58.

FANTOM5 (CAGE): breadth tissue_specific, TPM avg 0.1672 / max 152.4667, expressed in 4 samples.

FANTOM5 promoters (2 alternative TSS)

Promoter ID	TPM avg	Samples expressed
186033	0.1604	4
186034	0.0069	3

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
sperm	CL:0000019	96.58	gold quality
left testis	UBERON:0004533	94.00	gold quality
right testis	UBERON:0004534	93.88	gold quality
testis	UBERON:0000473	91.23	gold quality
monocyte	CL:0000576	84.84	gold quality
leukocyte	CL:0000738	84.40	gold quality
adult organism	UBERON:0007023	83.79	gold quality
granulocyte	CL:0000094	77.21	gold quality
blood	UBERON:0000178	76.44	gold quality
bone marrow	UBERON:0002371	68.67	gold quality
vermiform appendix	UBERON:0001154	68.25	gold quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	67.25	gold quality
pancreatic ductal cell	CL:0002079	66.10	silver quality
ileal mucosa	UBERON:0000331	64.71	silver quality
spleen	UBERON:0002106	62.63	gold quality
tibialis anterior	UBERON:0001385	62.38	silver quality
caecum	UBERON:0001153	62.19	gold quality
bone marrow cell	CL:0002092	61.65	silver quality
right lung	UBERON:0002167	57.39	gold quality
epithelial cell of pancreas	CL:0000083	55.39	gold quality
cardiac muscle of right atrium	UBERON:0003379	54.34	gold quality
left ventricle myocardium	UBERON:0006566	54.23	gold quality
upper leg skin	UBERON:0004262	54.11	silver quality
deltoid	UBERON:0001476	53.96	gold quality
kidney epithelium	UBERON:0004819	53.93	gold quality
upper arm skin	UBERON:0004263	53.52	gold quality
mucosa of stomach	UBERON:0001199	53.43	gold quality
upper lobe of left lung	UBERON:0008952	51.78	gold quality
upper lobe of lung	UBERON:0008948	51.70	gold quality
lymph node	UBERON:0000029	51.47	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	no	1.44

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

15 targeting SIRPD, 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-4697-3P	99.89	67.09	1123
HSA-MIR-605-3P	99.88	69.22	1833
HSA-MIR-3121-3P	99.82	71.96	3630
HSA-MIR-5701	98.97	69.54	1502
HSA-MIR-6846-5P	98.81	65.86	1121
HSA-MIR-6848-5P	98.81	65.49	1126
HSA-MIR-4635	98.74	67.63	1339
HSA-MIR-4726-3P	98.49	63.89	1385
HSA-MIR-7113-5P	97.88	67.33	1735
HSA-MIR-9851-5P	97.57	67.49	1067
HSA-MIR-5702	96.68	68.21	958
HSA-MIR-711	96.60	65.75	528
HSA-MIR-1237-5P	95.38	62.21	451
HSA-MIR-4488	95.38	62.00	443
HSA-MIR-4697-5P	95.38	61.72	457

Cross-species orthologs

0 orthologs

Paralogs (4): SIRPG (ENSG00000089012), SIRPB1 (ENSG00000101307), SIRPB2 (ENSG00000196209), SIRPA (ENSG00000198053)

Protein

Protein identifiers

Signal-regulatory protein delta — Q9H106 (reviewed: Q9H106)

Alternative names: Protein tyrosine phosphatase non-receptor type substrate 1-like 2

All UniProt accessions (3): Q9H106, H0Y747, Q5TFQ5

UniProt curated annotations — full annotation on UniProt →

Subcellular location. Secreted.

RefSeq proteins (2): NP_001397731, NP_848555* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR003599	Ig_sub	Domain
IPR007110	Ig-like_dom	Domain
IPR013106	Ig_V-set	Domain
IPR013783	Ig-like_fold	Homologous_superfamily
IPR036179	Ig-like_dom_sf	Homologous_superfamily
IPR051755	Ig-like_CS_Receptor	Family

Pfam: PF07686

UniProt features (7 total): signal peptide 1, chain 1, domain 1, region of interest 1, glycosylation site 1, disulfide bond 1, sequence variant 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q9H106-F1	80.02	0.54

Functional residue map

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

Disulfide bonds (1): 51–117

Glycosylation sites (1): 174

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 22 (showing top): ZWANG_TRANSIENTLY_UP_BY_2ND_EGF_PULSE_ONLY, GLI1_TARGET_GENES, ZNF175_TARGET_GENES, ZNF22_TARGET_GENES, GSE11864_UNTREATED_VS_CSF1_IFNG_IN_MAC_UP, MIR4697_3P, MIR6846_5P, MIR6848_5P, chr20p13, NOTCH3_TARGET_GENES, ZAK_PBMC_MRKAD5_HIV_1_GAG_POL_NEF_AGE_20_50YO_1DY_UP, KENNEDY_PBMC_DRYVAX_AGE_18_40YO_STIMULATED_VS_UNSTIMULATED_1_TO_48MO_TOP_DEG_DN, OSMAN_BLOOD_CHAD63_KH_AGE_18_50YO_HIGH_DOSE_SUBJECTS_24HR_UP, HARALAMBIEVA_PBMC_M_M_R_II_AGE_11_22YO_VACCINATED_VS_UNVACCINATED_7YR_DN, GSE17974_IL4_AND_ANTI_IL12_VS_UNTREATED_0.5H_ACT_CD4_TCELL_UP

GO Biological Process (0):

GO Molecular Function (0):

GO Cellular Component (2): extracellular region (GO:0005576), plasma membrane (GO:0005886)

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
cellular anatomical structure	1
membrane	1
cell periphery	1

Protein interactions and networks

STRING

1103 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
SIRPD	C2orf74	A8MZ97	570
SIRPD	SANBR	Q6NSI8	507
SIRPD	CD47	Q08722	482
SIRPD	FAM162B	Q5T6X4	477
SIRPD	MINDY4	Q4G0A6	419
SIRPD	NSFL1C	Q9UNZ2	377
SIRPD	TTLL9	Q3SXZ7	347
SIRPD	INMT	O95050	330
SIRPD	PLA2G15	Q8NCC3	329
SIRPD	OR7C1	O76099	323
SIRPD	NOL4	O94818	311
SIRPD	A0A0B4J1T7	A0A0B4J1T7	310
SIRPD	SEC31B	Q9NQW1	305
SIRPD	SURF6	O75683	305
SIRPD	TIMM44	O43615	301

IntAct

7 interactions, top by confidence:

A	B	Type	Score
SIRPD	HIKESHI	psi-mi:“MI:0914”(association)	0.530
SIRPD	IGSF10	psi-mi:“MI:0915”(physical association)	0.400
TERF1	SIRPD	psi-mi:“MI:0915”(physical association)	0.370
SIRPD	ADAM10	psi-mi:“MI:0914”(association)	0.350
SIRPD	FAT1	psi-mi:“MI:0914”(association)	0.350

BioGRID (89): EPDR1 (Affinity Capture-MS), DIRAS2 (Affinity Capture-MS), C11orf73 (Affinity Capture-MS), NT5C (Affinity Capture-MS), DIRAS2 (Affinity Capture-MS), NT5C (Affinity Capture-MS), C11orf73 (Affinity Capture-MS), EPDR1 (Affinity Capture-MS), PLXNA3 (Affinity Capture-MS), PCSK6 (Affinity Capture-MS), SUN2 (Affinity Capture-MS), P3H4 (Affinity Capture-MS), THBS1 (Affinity Capture-MS), ADAMTS7 (Affinity Capture-MS), TTC13 (Affinity Capture-MS)

ESM2 similar proteins: A4D1S0, A4K2S4, A6NMD0, B9A064, F8WCM5, H7C350, O00220, O14931, O15533, O70146, O73895, O75298, O76081, P01854, P01883, P14138, P15692, P15814, P16382, P20764, P24394, P49763, P61484, P83743, Q00731, Q0VCS0, Q15569, Q3UM83, Q5R8H1, Q5RFR2, Q5TJE4, Q63257, Q63572, Q68D85, Q6P050, Q6PZD2, Q6WG24, Q7TQM3, Q863Z5, Q8MJ02

Diamond homologs: O00241, O46631, P01691, P01844, P01845, P01847, P01915, P04230, P04231, P18211, P18468, P18469, P18470, P20040, P78324, P97710, P97797, Q5JXA9, Q5TFQ8, Q9H106, Q9P1W8, Q9PWR4, P55899, Q29980, P01835, P35737, P01634, P01645, P01646, P01861, P20760, P01693, P01635, P01683, P14432

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	27
Likely benign	3
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

550 predictions. Top by Δscore:

Variant	Effect	Δscore
20:1551683:ATACT:A	donor_loss	0.8800
20:1551684:TAC:T	donor_loss	0.8800
20:1551685:AC:A	donor_loss	0.8800
20:1551686:CTC:C	donor_loss	0.8800
20:1551687:TCAC:T	donor_loss	0.8800
20:1551688:C:CG	donor_loss	0.8800
20:1551689:ACCA:A	donor_loss	0.8800
20:1552036:CTC:C	acceptor_gain	0.8800
20:1551682:CATA:C	donor_loss	0.8700
20:1551782:A:T	acceptor_gain	0.8600
20:1551715:G:GT	donor_gain	0.8500
20:1551715:G:T	donor_loss	0.8500
20:1551743:T:TA	donor_gain	0.8500
20:1534442:C:CC	acceptor_gain	0.8400
20:1540242:T:A	donor_gain	0.8400
20:1534438:AAGCC:A	acceptor_loss	0.8100
20:1534439:AGCC:A	acceptor_loss	0.8100
20:1534440:GCCTG:G	acceptor_loss	0.8100
20:1534441:CCTGA:C	acceptor_loss	0.8100
20:1534442:C:T	acceptor_loss	0.8100
20:1534443:T:G	acceptor_loss	0.8100
20:1534447:A:C	acceptor_loss	0.8000
20:1534450:CAA:C	acceptor_loss	0.8000
20:1534451:A:T	acceptor_loss	0.8000
20:1551730:C:CA	donor_gain	0.8000
20:1534444:G:C	acceptor_loss	0.7900
20:1534452:A:C	acceptor_loss	0.7900
20:1551872:T:TG	acceptor_gain	0.7900
20:1540157:G:A	donor_gain	0.7800
20:1534445:AAA:A	acceptor_loss	0.7700

AlphaMissense

1251 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
20:1551812:A:C	F100L	0.949
20:1551812:A:T	F100L	0.949
20:1551814:A:G	F100L	0.949
20:1551917:G:C	F65L	0.940
20:1551917:G:T	F65L	0.940
20:1551919:A:G	F65L	0.940
20:1551752:G:C	F120L	0.915
20:1551752:G:T	F120L	0.915
20:1551754:A:G	F120L	0.915
20:1551878:G:C	F78L	0.898
20:1551878:G:T	F78L	0.898
20:1551880:A:G	F78L	0.898
20:1551863:A:C	F83L	0.871
20:1551863:A:T	F83L	0.871
20:1551865:A:G	F83L	0.871
20:1551914:C:A	K66N	0.869
20:1551914:C:G	K66N	0.869
20:1551920:C:A	W64C	0.868
20:1551920:C:G	W64C	0.868
20:1551755:C:A	K119N	0.852
20:1551755:C:G	K119N	0.852
20:1551918:A:G	F65S	0.833
20:1551966:A:G	L49S	0.828
20:1552022:G:C	F30L	0.822
20:1552022:G:T	F30L	0.822
20:1552024:A:G	F30L	0.822
20:1551918:A:C	F65C	0.818
20:1551922:A:G	W64R	0.810
20:1551922:A:T	W64R	0.810
20:1551753:A:C	F120C	0.805

dbSNP variants (sampled 300 via entrez): RS1000095936 (20:1545681 T>C), RS1000194893 (20:1539936 C>T), RS1000203788 (20:1550109 T>G), RS1000220917 (20:1540198 C>A), RS1000376837 (20:1544496 T>G), RS1000524067 (20:1541324 A>G), RS1000555092 (20:1541642 C>A), RS1000741014 (20:1535483 G>T), RS1000918629 (20:1539445 G>A,T), RS1001070034 (20:1535176 T>A), RS1001143556 (20:1555776 T>A), RS1001241482 (20:1551514 CTT>C,CTTT), RS1001353845 (20:1545270 C>G,T), RS1001457145 (20:1557847 G>C), RS1001689865 (20:1546602 C>A)

Disease associations

OMIM: gene MIM:621320 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

4 associations (top):

Study	Trait	p-value
GCST004599_202	Mean platelet volume	6.000000e-33
GCST004607_25	Plateletcrit	1.000000e-15
GCST004616_49	Platelet distribution width	5.000000e-12
GCST011096_27	Systemic lupus erythematosus	3.000000e-08

EFO canonical traits (2, from GWAS)

EFO ID	Trait name
EFO:0007985	platelet crit
EFO:0007984	platelet component distribution width

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

9 total (human), top 9 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
propionaldehyde	decreases expression	1
sulforaphane	increases expression	1
3,4,5,3’,4’-pentachlorobiphenyl	decreases expression	1
CGP 52608	affects binding, increases reaction	1
Benzo(a)pyrene	increases methylation	1
Ethyl Methanesulfonate	decreases expression	1
Methyl Methanesulfonate	decreases expression	1
Tretinoin	increases expression	1
Valproic Acid	increases methylation	1

Clinical trials (associated diseases)

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