SH2D7

Summary

SH2D7 (SH2 domain containing 7, HGNC:34549) is a protein-coding gene on chromosome 15q25.1, encoding SH2 domain-containing protein 7 (A6NKC9).

Predicted to be active in cytoplasm.

Source: NCBI Gene 646892 — RefSeq curated summary.

At a glance

• GWAS associations: 3
• Clinical variants (ClinVar): 78 total
• MANE Select transcript: NM_001101404

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:34549
Approved symbol	SH2D7
Name	SH2 domain containing 7
Location	15q25.1
Locus type	gene with protein product
Status	Approved
Aliases	LOC646892
Ensembl gene	ENSG00000183476
Ensembl biotype	protein_coding
Entrez	646892

Gene structure

Transcript identifiers

Ensembl transcripts: 2 — 2 protein_coding

ENST00000328828, ENST00000409568

RefSeq mRNA: 1 — MANE Select: NM_001101404 NM_001101404

CCDS: CCDS45315

Canonical transcript exons

ENST00000328828 — 6 exons

Exon	Start	End
ENSE00001303333	78100899	78101558
ENSE00001375197	78098384	78098596
ENSE00001580939	78103465	78104362
ENSE00001698307	78094112	78094201
ENSE00001786926	78092561	78092760
ENSE00003504480	78097929	78098094

Expression profiles

Bgee: expression breadth broad, 82 present calls, max score 77.59.

FANTOM5 (CAGE): breadth tissue_specific, TPM avg 0.0801 / max 49.6193, expressed in 9 samples.

FANTOM5 promoters (3 alternative TSS)

Promoter ID	TPM avg	Samples expressed
147882	0.0448	3
147886	0.0240	6
147881	0.0113	3

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	77.59	gold quality
mucosa of transverse colon	UBERON:0004991	77.13	gold quality
duodenum	UBERON:0002114	67.49	gold quality
ventricular zone	UBERON:0003053	65.51	gold quality
ganglionic eminence	UBERON:0004023	65.21	gold quality
cortical plate	UBERON:0005343	62.71	gold quality
testis	UBERON:0000473	62.48	gold quality
left testis	UBERON:0004533	62.33	gold quality
right testis	UBERON:0004534	61.79	gold quality
transverse colon	UBERON:0001157	60.47	gold quality
small intestine	UBERON:0002108	57.77	gold quality
colonic epithelium	UBERON:0000397	57.37	gold quality
small intestine Peyer’s patch	UBERON:0003454	56.94	gold quality
intestine	UBERON:0000160	54.32	gold quality
colon	UBERON:0001155	53.29	gold quality
stromal cell of endometrium	CL:0002255	52.51	silver quality
placenta	UBERON:0001987	52.46	gold quality
anterior cingulate cortex	UBERON:0009835	50.77	gold quality
temporal lobe	UBERON:0001871	49.92	gold quality
amygdala	UBERON:0001876	49.86	gold quality
prefrontal cortex	UBERON:0000451	49.78	gold quality
rectum	UBERON:0001052	48.91	gold quality
cerebral cortex	UBERON:0000956	47.93	gold quality
vermiform appendix	UBERON:0001154	47.82	gold quality
frontal cortex	UBERON:0001870	47.70	gold quality
gall bladder	UBERON:0002110	46.96	gold quality
smooth muscle tissue	UBERON:0001135	46.88	gold quality
Ammon’s horn	UBERON:0001954	46.69	gold quality
dorsolateral prefrontal cortex	UBERON:0009834	46.63	gold quality
urinary bladder	UBERON:0001255	46.32	silver quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-MTAB-8410	yes	4.50
E-ANND-3	yes	3.77

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

32 targeting SH2D7, 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-302E	99.96	70.74	2669
HSA-MIR-302A-3P	99.89	71.23	1777
HSA-MIR-302B-3P	99.89	71.23	1777
HSA-MIR-302C-3P	99.89	71.20	1778
HSA-MIR-302D-3P	99.89	71.25	1777
HSA-MIR-4728-5P	99.85	69.39	4718
HSA-MIR-373-3P	99.84	70.68	1668
HSA-MIR-520E-3P	99.84	70.55	1698
HSA-MIR-372-3P	99.83	70.58	1691
HSA-MIR-520A-3P	99.83	70.59	1687
HSA-MIR-520B-3P	99.83	70.56	1699
HSA-MIR-520C-3P	99.83	70.56	1699
HSA-MIR-520D-3P	99.83	70.78	1676
HSA-MIR-6785-5P	99.82	68.68	4428
HSA-MIR-1273H-5P	99.77	66.32	2471
HSA-MIR-6715B-5P	99.64	69.63	1420
HSA-MIR-4269	99.55	69.89	1373
HSA-MIR-7106-5P	99.53	67.47	3574
HSA-MIR-3612	99.45	66.02	1333
HSA-MIR-650	99.45	65.77	1309
HSA-MIR-128-1-5P	99.33	60.46	332
HSA-MIR-128-2-5P	99.33	60.83	311
HSA-MIR-4667-3P	99.26	65.45	1608
HSA-MIR-2467-3P	98.65	67.18	1969
HSA-MIR-548S	98.50	67.17	1213
HSA-MIR-1914-5P	97.83	66.21	807
HSA-MIR-204-3P	97.80	66.84	1656
HSA-MIR-4646-5P	97.70	66.84	1692
HSA-MIR-3137	97.26	66.78	761
HSA-MIR-4435	95.90	65.47	1201

Cross-species orthologs

4 orthologs

Organism	Symbol	Gene ID
danio_rerio	sh2d7	ENSDARG00000088167
mus_musculus	Sh2d7	ENSMUSG00000046460
rattus_norvegicus	Sh2d7	ENSRNOG00000023870
caenorhabditis_elegans		WBGENE00008733

Paralogs (4): SH2D2A (ENSG00000027869), SH2D4A (ENSG00000104611), SH2D4B (ENSG00000178217), HSH2D (ENSG00000196684)

Protein

Protein identifiers

SH2 domain-containing protein 7 — A6NKC9 (reviewed: A6NKC9)

All UniProt accessions (2): A6NKC9, B8ZZB5

RefSeq proteins (1): NP_001094874* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR000980	SH2	Domain
IPR035885	SH2D7_SH2	Domain
IPR036860	SH2_dom_sf	Homologous_superfamily

Pfam: PF00017

UniProt features (11 total): compositionally biased region 4, region of interest 3, sequence variant 2, chain 1, domain 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-A6NKC9-F1	57.93	0.18

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 10 (showing top): FOXD2_TARGET_GENES, HAND1_TARGET_GENES, ZNF2_TARGET_GENES, ZNF282_TARGET_GENES, MIR1914_5P, MIR1298_3P, GOMF_MOLECULAR_ADAPTOR_ACTIVITY, GAO_LARGE_INTESTINE_ADULT_CE_OLFM4HIGH_STEM_CELL, BARHL1_TARGET_GENES, chr15q25

GO Biological Process (0):

GO Molecular Function (0):

GO Cellular Component (1): cytoplasm (GO:0005737)

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
intracellular anatomical structure	1
cellular anatomical structure	1

Protein interactions and networks

STRING

248 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
SH2D7	C3orf22	Q8N5N4	596
SH2D7	RNASE12	Q5GAN4	571
SH2D7	C12orf56	Q8IXR9	571
SH2D7	SMIM17	P0DL12	543
SH2D7	TMEM45B	Q96B21	542
SH2D7	IRAG2	Q12912	519
SH2D7	TSPAN6	O43657	514
SH2D7	CC2D2B	Q6DHV5	508
SH2D7	ANKRD62	A6NC57	507
SH2D7	C1orf167	Q5SNV9	507
SH2D7	C22orf42	Q6IC83	507
SH2D7	SPDYE4	A6NLX3	506
SH2D7	CLPSL1	A2RUU4	480
SH2D7	EPCIP	Q9NYP8	480
SH2D7	RD3L	P0DJH9	479
SH2D7	SMIM21	Q3B7S5	479

IntAct

0 interactions, top by confidence:

BioGRID (1): SH2D7 (Cross-Linking-MS (XL-MS))

ESM2 similar proteins: A2A7Y5, A6NKC9, B1ASB6, F1MGG3, M3WHG5, O54824, O88834, P15391, P24394, P25917, P25918, P27987, P60669, Q13796, Q14005, Q32PJ7, Q3LRP3, Q49AM3, Q4R2Z8, Q5FVQ5, Q5JXC2, Q6VYH9, Q6ZMY3, Q7M4L6, Q7Z591, Q7Z6P3, Q80VR2, Q80VW7, Q863Z5, Q8BG26, Q8BI17, Q8BLR5, Q8BZW2, Q8C886, Q8CB87, Q8IY92, Q8NAV2, Q8NDX1, Q8NHY3, Q8R2H3

Diamond homologs: A6NKC9, A6X942, G5ECJ6, O08908, O88834, P03949, P46109, P47941, Q00655, Q08012, Q08CX2, Q56A36, Q5SQS7, Q5U2U2, Q6AYC8, Q6VYH9, Q6YKA8, Q8BI17, Q8UUU2, Q96JZ2, Q9D7V1, Q9H788, Q9NP31, Q9QXK9, P00519, P00520, P00521, P10447, P20936, P29353, P32577, P41239, P41240, P41241, P42684, P50904, P98083, Q03160, Q0IIE2, Q0VBZ0

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	72
Likely benign	4
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

1193 predictions. Top by Δscore:

Variant	Effect	Δscore
15:78092757:GCAA:G	donor_gain	1.0000
15:78092761:G:GG	donor_gain	1.0000
15:78098044:G:GT	donor_gain	1.0000
15:78098093:GG:G	donor_gain	1.0000
15:78098094:GG:G	donor_gain	1.0000
15:78098095:G:GC	donor_loss	1.0000
15:78098096:T:G	donor_loss	1.0000
15:78092758:C:T	donor_gain	0.9900
15:78092760:AGTA:A	donor_loss	0.9900
15:78092762:T:G	donor_loss	0.9900
15:78094197:TACAG:T	donor_loss	0.9900
15:78094198:ACAGG:A	donor_loss	0.9900
15:78094199:CAGG:C	donor_loss	0.9900
15:78094200:AG:A	donor_loss	0.9900
15:78094201:GG:G	donor_loss	0.9900
15:78094202:GTA:G	donor_loss	0.9900
15:78094203:T:A	donor_loss	0.9900
15:78097927:A:AG	acceptor_gain	0.9900
15:78097927:AG:A	acceptor_gain	0.9900
15:78097927:AGG:A	acceptor_gain	0.9900
15:78097928:G:GG	acceptor_gain	0.9900
15:78097928:GG:G	acceptor_gain	0.9900
15:78097928:GGG:G	acceptor_gain	0.9900
15:78098095:G:GG	donor_gain	0.9900
15:78098374:A:AG	acceptor_gain	0.9900
15:78098374:AT:A	acceptor_gain	0.9900
15:78098375:T:G	acceptor_gain	0.9900
15:78100894:CCCA:C	acceptor_loss	0.9900
15:78100896:CA:C	acceptor_loss	0.9900
15:78100897:A:AG	acceptor_gain	0.9900

AlphaMissense

2949 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
15:78094152:T:C	F73L	0.996
15:78094154:C:A	F73L	0.996
15:78094154:C:G	F73L	0.996
15:78092735:T:A	W51R	0.989
15:78092735:T:C	W51R	0.989
15:78094192:T:C	L86S	0.985
15:78097951:T:C	F97L	0.985
15:78097953:T:A	F97L	0.985
15:78097953:T:G	F97L	0.985
15:78092684:T:C	F34L	0.983
15:78092686:C:A	F34L	0.983
15:78092686:C:G	F34L	0.983
15:78092738:T:C	F52L	0.983
15:78092740:T:A	F52L	0.983
15:78092740:T:G	F52L	0.983
15:78094153:T:C	F73S	0.983
15:78097950:T:A	H96Q	0.979
15:78097950:T:G	H96Q	0.979
15:78094195:C:T	S87F	0.978
15:78092739:T:C	F52S	0.977
15:78094147:G:T	G71V	0.973
15:78098062:T:C	F134L	0.973
15:78098064:C:A	F134L	0.973
15:78098064:C:G	F134L	0.973
15:78092685:T:C	F34S	0.971
15:78092756:C:A	R58S	0.969
15:78092747:T:C	F55L	0.968
15:78092749:C:A	F55L	0.968
15:78092749:C:G	F55L	0.968
15:78094159:T:A	I75N	0.968

dbSNP variants (sampled 300 via entrez): RS1000086620 (15:78095561 T>C), RS1000229205 (15:78089927 G>T), RS1000359340 (15:78095859 T>C), RS1000530432 (15:78100334 T>A,C), RS1000568180 (15:78091360 C>T), RS1000734207 (15:78097598 T>C), RS1001000405 (15:78093549 C>G), RS1001252771 (15:78088722 A>G), RS1001510097 (15:78103119 C>G), RS1001883036 (15:78099589 A>C), RS1001895689 (15:78104716 C>T), RS1001976344 (15:78099925 C>T), RS1002221440 (15:78093481 T>C), RS1002488997 (15:78093154 G>A), RS1002866366 (15:78104500 G>A)

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

3 associations (top):

Study	Trait	p-value
GCST003476_6	Eyebrow thickness	1.000000e-06
GCST006103_14	Interleukin-6 levels	8.000000e-07
GCST008502_13	Low susceptibility to hepatitis C infection	6.000000e-06

EFO canonical traits (2, from GWAS)

EFO ID	Trait name
EFO:0004810	interleukin-6 measurement
EFO:0010101	decreased susceptibility to hepatitis C infection

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

12 total (human), top 12 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
fluorene-9-bisphenol	decreases expression	1
bisphenol A	affects cotreatment, decreases methylation	1
benzo(e)pyrene	decreases methylation	1
aflatoxin B2	decreases methylation	1
S-(1,2-dichlorovinyl)cysteine	affects cotreatment, affects response to substance, increases expression	1
abrine	increases expression	1
theaflavin-3,3’-digallate	affects expression	1
Fulvestrant	affects cotreatment, decreases methylation	1
Benzo(a)pyrene	affects methylation, decreases methylation	1
Lipopolysaccharides	affects response to substance, increases expression, affects cotreatment	1
Methapyrilene	decreases methylation	1
Tobacco Smoke Pollution	increases methylation	1

Clinical trials (associated diseases)

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