GPATCH11

Summary

GPATCH11 (G-patch domain containing 11, HGNC:26768) is a protein-coding gene on chromosome 2p22.2, encoding G patch domain-containing protein 11 (Q8N954).

Predicted to enable nucleic acid binding activity. Located in kinetochore and nucleoplasm.

Source: NCBI Gene 253635 — automated summary from GO annotations (Alliance of Genome Resources).

At a glance

• Gene–disease (curated): neurodevelopmental disorder (Strong, GenCC)
• Clinical variants (ClinVar): 51 total — 4 pathogenic
• GTEx eGene: eQTL in 26 tissues, sQTL in 3 (q < 0.05)
• Constraint (gnomAD): pLI 0.00 (LoF-tolerant), LOEUF 1.01 (unconstrained)
• MANE Select transcript: NM_174931

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:26768
Approved symbol	GPATCH11
Name	G-patch domain containing 11
Location	2p22.2
Locus type	gene with protein product
Status	Approved
Aliases	FLJ38348, CENPY, CENP-Y
Ensembl gene	ENSG00000152133
Ensembl biotype	protein_coding
OMIM	621183
Entrez	253635

Gene structure

Transcript identifiers

Ensembl transcripts: 8 — 7 protein_coding, 1 retained_intron

MANE Select: ENST00000674370

Transcript support level (Ensembl TSL; 1 = fully mRNA-supported): TSL 1: 1, TSL 3: 1

ENST00000674370, ENST00000281932, ENST00000473067, ENST00000964376, ENST00000964377, ENST00001021501, ENST00001129590, ENST00001137545

RefSeq mRNA: 9 — MANE Select: NM_174931 NM_001278505, NM_001322249, NM_001371856, NM_001371858, NM_001371859, NM_001371860, NM_001371861, NM_001371862, NM_174931

CCDS: CCDS1785

Canonical transcript exons

ENST00000674370 — 9 exons

Exon	Start	End
ENSE00001153301	37094082	37094195
ENSE00001213466	37095437	37095518
ENSE00001427985	37089640	37089866
ENSE00001480030	37090681	37090722
ENSE00001583953	37096208	37099244
ENSE00001951164	37084518	37084570
ENSE00003520100	37091916	37092036
ENSE00003617907	37092165	37092255
ENSE00003898684	37088369	37088440

Expression profiles

Bgee: expression breadth ubiquitous, 254 present calls, max score 90.07.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 16.1036 / max 832.5096, expressed in 1734 samples.

Highest expression (Bgee): calcaneal tendon, middle temporal gyrus, pancreatic ductal cell, tendon, male germ line stem cell (sensu Vertebrata) in testis.

Genetic regulation across tissues (GTEx eQTL / sQTL)

GPATCH11 is an eGene in GTEx v10 — its expression is genetically regulated (eQTL) in 26 tissues and its splicing (sQTL) in 3 (q < 0.05). Strongest associations first; slope = normalized effect of the lead variant’s alternative allele.

showing 20 of 29 significant tissue × QTL associations:

Tissue	QTL	q-value	Slope	Lead variant
Cells Cultured fibroblasts	eqtl	4.9e-26	+0.22	2:37097965:T:C
Testis	sqtl	4.4e-19	-1.08	2:37096284:A:G
Artery Tibial	eqtl	1.3e-15	+0.21	2:37097965:T:C
Spleen	eqtl	4.5e-09	+0.32	2:37090314:A:C
Esophagus Muscularis	eqtl	9.8e-09	+0.18	2:37097965:T:C
Esophagus Mucosa	eqtl	2.0e-07	+0.16	2:37097965:T:C
Skin Sun Exposed Lower leg	eqtl	1.6e-06	-0.14	2:37141907:T:C
Stomach	eqtl	6.4e-06	+0.22	2:37097965:T:C
Colon Transverse	eqtl	5.0e-05	+0.16	2:37097965:T:C
Whole Blood	eqtl	5.2e-05	+0.11	2:37097965:T:C
Esophagus Gastroesophageal Junction	eqtl	1.9e-04	+0.18	2:37097965:T:C
Colon Sigmoid	eqtl	3.7e-04	+0.18	2:37097965:T:C
Artery Aorta	eqtl	6.7e-04	+0.14	2:37097965:T:C
Skin Not Sun Exposed Suprapubic	eqtl	8.1e-04	-0.13	2:37075037:T:C
Thyroid	eqtl	1.3e-03	+0.13	2:37097965:T:C
Nerve Tibial	eqtl	1.7e-03	+0.12	2:37097965:T:C
Cells EBV-transformed lymphocytes	eqtl	3.1e-03	-0.18	2:37129849:C:T
Cells EBV-transformed lymphocytes	sqtl	4.8e-03	+1.96	2:36085101:A:T
Adipose Subcutaneous	eqtl	5.4e-03	+0.09	2:37097965:T:C
Brain Putamen basal ganglia	eqtl	5.9e-03	-0.27	2:37129412:C:A

FANTOM5 promoters

5 alternative TSS:

Promoter ID	TPM avg	Samples expressed
19749	14.3955	1715
19746	0.7146	296
19748	0.6097	307
202159	0.2651	121
19747	0.1187	50

Top tissues by expression

showing 100 of 256 tissues by Bgee expression score (0-100, higher = more expressed):

Tissue	Anatomy ID	Expression score	Quality
calcaneal tendon	UBERON:0003701	90.07	gold quality
middle temporal gyrus	UBERON:0002771	87.46	gold quality
pancreatic ductal cell	CL:0002079	86.92	gold quality
tendon	UBERON:0000043	85.51	gold quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	85.14	gold quality
endothelial cell	CL:0000115	84.85	gold quality
cardiac muscle of right atrium	UBERON:0003379	84.59	silver quality
adipose tissue	UBERON:0001013	84.25	gold quality
upper arm skin	UBERON:0004263	84.23	silver quality
postcentral gyrus	UBERON:0002581	83.69	gold quality
Brodmann (1909) area 23	UBERON:0013554	83.64	gold quality
superior frontal gyrus	UBERON:0002661	83.20	gold quality
myocardium	UBERON:0002349	83.16	silver quality
medial globus pallidus	UBERON:0002477	82.92	gold quality
subcutaneous adipose tissue	UBERON:0002190	82.74	gold quality
entorhinal cortex	UBERON:0002728	82.70	gold quality
lymph node	UBERON:0000029	82.67	gold quality
C1 segment of cervical spinal cord	UBERON:0006469	82.67	gold quality
ventricular zone	UBERON:0003053	82.57	gold quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	82.51	gold quality
corpus callosum	UBERON:0002336	82.40	gold quality
tendon of biceps brachii	UBERON:0008188	82.40	gold quality
parietal lobe	UBERON:0001872	82.32	gold quality
prefrontal cortex	UBERON:0000451	82.22	gold quality
primary visual cortex	UBERON:0002436	82.20	gold quality
spinal cord	UBERON:0002240	82.06	gold quality
globus pallidus	UBERON:0001875	81.54	gold quality
islet of Langerhans	UBERON:0000006	81.48	gold quality
cortical plate	UBERON:0005343	81.36	gold quality
ganglionic eminence	UBERON:0004023	81.23	gold quality
epithelial cell of pancreas	CL:0000083	81.17	silver quality
leukocyte	CL:0000738	81.11	gold quality
thoracic mammary gland	UBERON:0005200	81.08	gold quality
mammary gland	UBERON:0001911	81.04	gold quality
tonsil	UBERON:0002372	80.98	gold quality
frontal cortex	UBERON:0001870	80.93	gold quality
monocyte	CL:0000576	80.91	gold quality
bone marrow	UBERON:0002371	80.88	gold quality
Ammon’s horn	UBERON:0001954	80.81	gold quality
substantia nigra	UBERON:0002038	80.79	gold quality
epithelium of mammary gland	UBERON:0003244	80.78	gold quality
neocortex	UBERON:0001950	80.76	gold quality
cerebral cortex	UBERON:0000956	80.75	gold quality
mammary duct	UBERON:0001765	80.74	gold quality
occipital lobe	UBERON:0002021	80.58	gold quality
temporal lobe	UBERON:0001871	80.52	gold quality
nucleus accumbens	UBERON:0001882	80.52	gold quality
dorsolateral prefrontal cortex	UBERON:0009834	80.50	gold quality
midbrain	UBERON:0001891	80.26	gold quality
caudate nucleus	UBERON:0001873	80.17	gold quality
Brodmann (1909) area 9	UBERON:0013540	80.10	gold quality
adipose tissue of abdominal region	UBERON:0007808	80.01	gold quality
putamen	UBERON:0001874	79.94	gold quality
hypothalamus	UBERON:0001898	79.88	gold quality
vermiform appendix	UBERON:0001154	79.87	gold quality
brain	UBERON:0000955	79.82	gold quality
forebrain	UBERON:0001890	79.76	gold quality
trabecular bone tissue	UBERON:0002483	79.76	gold quality
anterior cingulate cortex	UBERON:0009835	79.68	gold quality
amygdala	UBERON:0001876	79.63	gold quality
bone marrow cell	CL:0002092	79.53	gold quality
cerebellum	UBERON:0002037	79.53	gold quality
cerebellar hemisphere	UBERON:0002245	79.43	gold quality
cerebellar cortex	UBERON:0002129	79.41	gold quality
buccal mucosa cell	CL:0002336	79.32	silver quality
omental fat pad	UBERON:0010414	79.32	gold quality
peritoneum	UBERON:0002358	79.30	gold quality
Brodmann (1909) area 46	UBERON:0006483	79.30	gold quality
colonic epithelium	UBERON:0000397	79.13	gold quality
adrenal tissue	UBERON:0018303	78.94	gold quality
granulocyte	CL:0000094	78.60	gold quality
oral cavity	UBERON:0000167	78.46	gold quality
caput epididymis	UBERON:0004358	78.38	gold quality
corpus epididymis	UBERON:0004359	78.27	gold quality
pons	UBERON:0000988	78.16	gold quality
pigmented layer of retina	UBERON:0001782	78.09	gold quality
right hemisphere of cerebellum	UBERON:0014890	78.05	gold quality
stromal cell of endometrium	CL:0002255	78.04	gold quality
synovial joint	UBERON:0002217	78.02	gold quality
right frontal lobe	UBERON:0002810	77.98	gold quality
cauda epididymis	UBERON:0004360	77.95	gold quality
secondary oocyte	CL:0000655	77.91	gold quality
substantia nigra pars reticulata	UBERON:0001966	77.89	gold quality
caecum	UBERON:0001153	77.78	gold quality
lower lobe of lung	UBERON:0008949	77.78	gold quality
layer of synovial tissue	UBERON:0007616	77.65	gold quality
eye	UBERON:0000970	77.57	gold quality
jejunal mucosa	UBERON:0000399	77.41	gold quality
palpebral conjunctiva	UBERON:0001812	77.41	gold quality
smooth muscle tissue	UBERON:0001135	77.39	gold quality
inferior vagus X ganglion	UBERON:0005363	77.31	gold quality
gingival epithelium	UBERON:0001949	76.98	silver quality
lateral globus pallidus	UBERON:0002476	76.98	gold quality
ileal mucosa	UBERON:0000331	76.97	gold quality
right adrenal gland cortex	UBERON:0035827	76.92	gold quality
adrenal gland	UBERON:0002369	76.86	gold quality
left adrenal gland	UBERON:0001234	76.66	gold quality
endometrium	UBERON:0001295	76.66	gold quality
gingiva	UBERON:0001828	76.63	gold quality
kidney epithelium	UBERON:0004819	76.61	silver quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	yes	4.20

HPA expression

RNA tissue specificity: Low tissue specificity

showing 60 of 80 HPA tissues / cells by nTPM:

Tissue / cell	Axis	nTPM	Protein (IHC)
Pons	tissue	33.9
Putamen	tissue	29.2
Cerebellum	tissue	27.5	high
Midbrain	tissue	27.4
Hypothalamus	tissue	27.4
Thalamus	tissue	27.2
Substantia nigra	tissue	27.0
Medulla oblongata	tissue	26.8
Corpus callosum	tissue	26.8
Periaqueductal gray	tissue	26.1
Prefrontal cortex	tissue	25.7
Cerebral cortex	tissue	25.7	high
Septum	tissue	25.7
Spinal cord	tissue	25.5
Occipital cortex	tissue	25.1
Superior colliculi	tissue	24.7
Hippocampal formation	tissue	24.6
Ventral forebrain	tissue	24.3
Retrosplenial and cingulate cortex	tissue	24.2
Motor cortex	tissue	24.0
Somatosensory cortex	tissue	23.6
Retrosplenial cortex	tissue	23.3
Basal ganglia	tissue	23.1	high
Entorhinal cortex	tissue	22.5
Temporal cortex	tissue	22.3
Adipose tissue	tissue	22.0	medium
Olfactory bulb	tissue	22.0
Amygdala	tissue	21.9
Insular cortex	tissue	21.2
Retina	tissue	19.5
Caudate putamen	tissue	16.8
Nucleus accumbens	tissue	14.4
Frontal cortex	tissue	13.4
Locus coeruleus	tissue	13.1
Postcentral gyrus	tissue	13.0
Lymph node	tissue	11.9	high
Hippocampus	tissue	11.7	high
Tonsil	tissue	11.0	high
Testis	tissue	10.9	high
Thymus	tissue	9.7
Bone marrow	tissue	9.5	high
Choroid plexus	tissue	9.1
Spleen	tissue	7.6	high
Appendix	tissue	7.4	high
Cervix	tissue	6.6	high
Breast	tissue	6.1	medium
Thyroid gland	tissue	6.0	high
Lung	tissue	5.9	high
Adrenal gland	tissue	5.9	high
Skin 1	tissue	5.6	high
Placenta	tissue	5.4	medium
Liver	tissue	5.4	medium
Parathyroid gland	tissue	5.2	low
Kidney	tissue	5.2	high
Heart muscle	tissue	5.1	medium
Tongue	tissue	5.1
Ovary	tissue	5.0	medium
Urinary bladder	tissue	4.9	high
Esophagus	tissue	4.8	high
Small intestine	tissue	4.7	high

Brain sub-regions (HPA Brain Atlas): detected in 192; highest nTPM — White matter (26.8), Ventral spinal cord (25.5), Dorsal hippocampus (24.6), Subiculum (24.2), Dorsal spinal cord (23.9).

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

Targeting GPATCH11 by miRDB confidence (max_score; target_count = how many genes the miRNA targets in total — lower means more specific).

showing 30 of 157 miRNAs:

miRNA	Max score	Avg score	miRNA target_count
HSA-MIR-5011-5P	100.00	83.46	5820
HSA-MIR-190A-3P	100.00	80.35	5520
HSA-MIR-7110-3P	100.00	73.18	2486
HSA-MIR-6873-3P	100.00	71.42	2626
HSA-MIR-4262	100.00	73.26	3931
HSA-MIR-340-5P	100.00	72.50	4437
HSA-MIR-432-3P	100.00	67.86	705
HSA-MIR-181A-5P	99.99	72.96	2995
HSA-MIR-181B-5P	99.99	72.97	2996
HSA-MIR-181C-5P	99.99	72.95	2996
HSA-MIR-181D-5P	99.99	73.04	2997
HSA-MIR-4789-5P	99.98	70.76	2721
HSA-MIR-433-3P	99.98	69.37	1203
HSA-MIR-23B-5P	99.98	66.07	587
HSA-MIR-548N	99.98	71.94	4170
HSA-MIR-4775	99.98	75.00	6394
HSA-MIR-12136	99.98	72.81	5713
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-607	99.97	73.62	5593
HSA-MIR-590-3P	99.96	74.34	6478
HSA-MIR-570-3P	99.96	72.41	4910
HSA-MIR-548AA	99.96	70.64	3753
HSA-MIR-548AP-3P	99.96	70.64	3753
HSA-MIR-548T-3P	99.96	70.64	3753
HSA-MIR-3658	99.96	73.87	4379
HSA-MIR-559	99.95	72.28	3609
HSA-MIR-548AB	99.95	71.31	3488
HSA-MIR-128-3P	99.95	71.17	2484

Functional genomics

gnomAD constraint: pLI 0.000444, LOEUF 1.01, missense Z -0.0808 — population loss-of-function intolerance (pLI ≥ 0.9 = LoF-intolerant; lower LOEUF = more constrained). gnomAD

Regional missense constraint (gnomAD RMC): no regional variation along ENST00000674370 — one region, missense o/e 1.07.

Cross-species orthologs

5 orthologs

Organism	Symbol	Gene ID
danio_rerio	gpatch11	ENSDARG00000026892
mus_musculus	Gpatch11	ENSMUSG00000050668
rattus_norvegicus	Gpatch11	ENSRNOG00000025317
drosophila_melanogaster	CG10053	FBGN0037490
caenorhabditis_elegans		WBGENE00011451

Additional cross-species homologs

Sequence homologs in species beyond Ensembl Compara’s model organisms, by Diamond local protein alignment (% sequence identity; best hit per species). Lower-identity rows are more distant homologs. The matched accessions’ gene symbols aren’t in biobtree yet, so each row shows the UniProt accession.

Organism	UniProt	Identity	Method
Saccharomyces cerevisiae YJM789	A6ZRL6	99.9%	Diamond
Saccharomyces cerevisiae S288C	P53866	99.9%	Diamond
Bos taurus	Q2KI19	93.8%	Diamond
Caenorhabditis briggsae	A8XYX2	89.8%	Diamond
Xenopus tropicalis	Q6DF57	66.1%	Diamond
Arabidopsis thaliana	Q94C11	50.0%	Diamond
Schizosaccharomyces pombe 972h-	C6Y4A5	41.7%	Diamond

Genomic neighbors (locus context)

Genes flanking this one on the chromosome (NCBI/Entrez gene neighborhood). Positional context only — some neighbors share regulatory elements (bidirectional promoters, antisense/overlapping transcripts), but chromosomal adjacency is not itself a functional relationship (see Interactions for that).

Symbol	Type	Entrez
CEBPZOS	protein-coding	100505876
CEBPZ	protein-coding	10153
PRKD3	protein-coding	23683
SULT6B1	protein-coding	391365
NDUFAF7	protein-coding	55471
EIF2AK2	protein-coding	5610
VIT	protein-coding	5212
HEATR5B	protein-coding	54497
STRN	protein-coding	6801

Protein

Protein identifiers

G patch domain-containing protein 11 — Q8N954 (reviewed: Q8N954)

Alternative names: Centromeric protein Y, Coiled-coil domain-containing protein 75

All UniProt accessions (2): A0A6I8PRS5, A0A6Q8JGY2

UniProt curated annotations — full annotation on UniProt →

Subcellular location. Chromosome. Centromere. Kinetochore.

Similarity. Belongs to the GPATCH11 family.

Isoforms (2)

UniProt ID	Names	Canonical?
Q8N954-1	1	yes
Q8N954-2	2

RefSeq proteins (9): NP_001265434, NP_001309178, NP_001358785, NP_001358787, NP_001358788, NP_001358789, NP_001358790, NP_001358791, NP_777591* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR000467	G_patch_dom	Domain
IPR025239	DUF4187	Domain
IPR039249	GPATCH11	Family

Pfam: PF01585, PF13821

UniProt features (10 total): region of interest 2, modified residue 2, splice variant 2, chain 1, domain 1, coiled-coil region 1, compositionally biased region 1

Structure

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q8N954-F1	80.60	0.42

Human Protein Atlas

Protein class: Predicted intracellular proteins

Protein evidence: Evidence at protein level

Subcellular location (HPA, imaging): nucleoplasm

Antibody reliability (HPA): IH enhanced · IF supported

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)

Type	Positions
Phosphoserine	141
N6-acetyllysine	149

Function

Pathways and Gene Ontology

Reactome pathways

0 curated (TAS) of 0; 0 disease pathways. Curated-first; evidence = TAS (manually curated) vs IEA (electronic inference).

MSigDB gene sets: 97 (showing top): FXR_IR1_Q6, TGCGCANK_UNKNOWN, CEBP_Q2, GGCKCATGS_UNKNOWN, RYTTCCTG_ETS2_B, FISCHER_DREAM_TARGETS, YNGTTNNNATT_UNKNOWN, GOCC_CHROMOSOMAL_REGION, GOCC_CONDENSED_CHROMOSOME_CENTROMERIC_REGION, CEBPB_02, chr2p22, GOCC_SUPRAMOLECULAR_COMPLEX, NRF1_Q6, HHEX_TARGET_GENES, HOXB4_TARGET_GENES

GO Molecular Function (1): nucleic acid binding (GO:0003676)

GO Cellular Component (2): kinetochore (GO:0000776), nucleoplasm (GO:0005654)

GO top-level categories

6 GO namespaces:

Category	Terms
binding	1
condensed chromosome, centromeric region	1
intracellular membraneless organelle	1
supramolecular complex	1
nuclear lumen	1
cellular anatomical structure	1

Experimentally-supported GO annotations

GO terms backed by direct experimental evidence (ECO experimental codes) — 1 of 3 annotations. The rest are phylogenetic / computational / electronic (IEA).

1 experimentally-supported GO terms:

GO term	NS	Evidence
kinetochore	CC	direct assay

Protein interactions and networks

STRING

showing 15 of 478 interactions by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
GPATCH11	YJU2B	P13994	555
GPATCH11	CCDC97	Q96F63	505
GPATCH11	U2SURP	O15042	487
GPATCH11	PDE12	Q6L8Q7	483
GPATCH11	PIGQ	Q9BRB3	471
GPATCH11	LIN52	Q52LA3	469
GPATCH11	WHR1	P49842	458
GPATCH11	NRDC	O43847	446
GPATCH11	PTBP3	O95758	442
GPATCH11	CEP128	Q6ZU80	435
GPATCH11	TECTB	Q96PL2	430
GPATCH11	TTC27	Q6P3X3	425
GPATCH11	CHERP	Q8IWX8	416
GPATCH11	FN3KRP	Q9HA64	410
GPATCH11	LEO1	Q8WVC0	404

IntAct

Human interaction partners of GPATCH11 in IntAct, one row per partner (best MIscore; records = supporting IntAct interaction records).

3 partners by confidence:

Partner	Interaction type	MIscore	Records
ADGRB3	physical association	0.560	3
SDCBP	physical association	0.560	3
RPLP2	physical association	0.400	1

BioGRID (81 interactions; top human partners by supporting records): RBM17 (Affinity Capture-MS; 3 records), SNRPA1 (Affinity Capture-MS; 3 records), SNRPF (Affinity Capture-MS; 3 records), ZRSR2 (Affinity Capture-MS; 3 records), DNAJC8 (Affinity Capture-MS; 2 records), RPLP2 (Cross-Linking-MS (XL-MS); 2 records), RPS8 (Affinity Capture-MS; 2 records), SDCBP (Two-hybrid; 2 records), SNRPB (Affinity Capture-MS; 2 records), SNRPB2 (Affinity Capture-MS; 2 records), SNRPE (Affinity Capture-MS; 2 records), SNRPG (Affinity Capture-MS; 2 records), SNRPN (Affinity Capture-MS; 2 records), STK4 (Affinity Capture-MS; 2 records), U2AF2 (Affinity Capture-MS; 2 records)

Disease & clinical

Genetic variants

Variant evidence for GPATCH11: 51 ClinVar records (4 pathogenic / likely pathogenic). Per-variant detail is on Sugi Variant.

ClinVar

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

Classification	Count (floor)
Pathogenic	4
Likely pathogenic	0
Uncertain significance	38
Likely benign	0
Benign	0

Top pathogenic / likely-pathogenic (4)

Showing all 4 pathogenic / likely-pathogenic ClinVar records, ranked by ClinVar review status (expert panel → multiple submitters → single submitter), then by number of submitting labs.

Variant ID	HGVS	Classification	Review	Submitters
3062155	NM_174931.4(GPATCH11):c.328+1G>T	Pathogenic	no assertion criteria provided	1
3062156	NM_174931.4(GPATCH11):c.454C>T (p.Arg152Ter)	Pathogenic	no assertion criteria provided	1
3062157	NM_174931.4(GPATCH11):c.449+1G>C	Pathogenic	no assertion criteria provided	1
3062158	NM_174931.4(GPATCH11):c.393C>G (p.Tyr131Ter)	Pathogenic	no assertion criteria provided	1

Per-variant reference — Sugi Variant

Explore GPATCH11’s pathogenic and likely-pathogenic variants individually — each with its ClinVar classification and conditions, applied ACMG criteria (ClinGen expert panel, where curated), the calibrated in-silico predictors (AlphaMissense, REVEL, SaProt, conservation), gnomAD frequency, and the predictor-disagreement QC signal — on Sugi Variant.

SpliceAI

Top 10 splice-impact sites by Δscore (adjacent positions with the same effect merged into one range; 36 predictions of 604):

Position(s)	Effect	Δscore	Sites
2:37091914–37091915	acceptor_loss	1.0000	6
2:37092032	donor_gain	1.0000
2:37092037–37092038	donor_loss	1.0000	6
2:37092160	acceptor_gain	1.0000
2:37092253	donor_gain	1.0000
2:37092256–37092257	donor_loss	1.0000	4
2:37094190	donor_gain	1.0000
2:37095435–37095436	acceptor_loss	1.0000	6
2:37095519–37095520	donor_loss	1.0000	5
2:37084571–37084572	donor_loss	0.9900	5

AlphaMissense

492 missense substitutions predicted likely pathogenic (of 1,757 scored), across 138 residues. Top 20 hotspot residues, ranked by the number of likely-pathogenic substitutions (of those reachable by a single-nucleotide change), then by mean score:

Residue	Likely-pathogenic substitutions	Mean am_pathogenicity	Max am_pathogenicity
M106	9	0.895	0.994
H284	8	0.984	0.993
D199	8	0.961	0.983
D32	8	0.927	0.979
D271	8	0.911	0.971
D187	8	0.802	0.929
C259	7	0.996	0.999
C262	7	0.995	0.998
C276	7	0.995	0.998
W261	7	0.990	0.997
C195	7	0.963	0.995
F171	7	0.960	0.992
F100	7	0.959	0.991
W211	7	0.943	0.992
M34	7	0.928	0.984
W213	7	0.923	0.973
N97	7	0.906	0.978
H256	7	0.878	0.975
G107	6	0.978	0.990
L103	6	0.954	0.999

HPA cancer prognostics

RNA cancer specificity: Low cancer specificity

Human Protein Atlas survival analysis — favorable = higher expression predicts better survival.

1 prognostic cancer types:

Cancer	Prognostic	p-value
Kidney Renal Clear Cell Carcinoma (TCGA)	favorable	2.82e-05

Disease associations

OMIM: gene MIM:621183 | disease phenotypes:

GenCC curated gene-disease

1 curated gene-disease records:

Disease	Classification	Inheritance	Records
neurodevelopmental disorder	Strong	Autosomal recessive

Genomics England panels (PanelApp)

Clinical diagnostic gene panels including this gene (5 panels, 4 green/diagnostic-grade). Confidence: green = diagnostic, amber = moderate.

5 panels:

Panel	Rating
Hypotonic infant	green
Intellectual disability	green
Leukodystrophy, childhood onset	green
Paediatric disorders	green
Retinal disorders	amber

Mondo (1): neurodevelopmental disorder (MONDO:0700092)

MeSH disease descriptors

1 disease descriptors:

Descriptor	Name	Tree numbers
D065886	Neurodevelopmental Disorders	F03.625

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

PharmGKB: 1 entry (CPIC guideline: no)

CTD chemical–gene interactions

27 total (human), top 27 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
FR900359	decreases phosphorylation	1
bisphenol F	affects expression, affects cotreatment	1
triphenyl phosphate	affects expression	1
arsenite	affects binding, increases reaction	1
tris(1,3-dichloro-2-propyl)phosphate	decreases expression	1
sodium arsenite	affects expression	1
resorcinol	decreases expression	1
di-n-butylphosphoric acid	affects expression	1
CGP 52608	affects binding, increases reaction	1
bisphenol S	affects cotreatment, decreases expression	1
MT19c compound	increases expression	1
Coumestrol	increases expression	1
Demecolcine	decreases expression	1
Dexamethasone	affects cotreatment, affects expression, decreases expression	1
Indomethacin	affects expression, decreases expression, affects cotreatment	1
Methyl Methanesulfonate	increases expression	1
Sodium Dodecyl Sulfate	decreases expression	1
Tobacco Smoke Pollution	increases expression	1
Tretinoin	decreases expression	1
Urethane	increases expression	1
Vincristine	decreases expression	1
1-Methyl-3-isobutylxanthine	affects cotreatment, affects expression, decreases expression	1
7,8-Dihydro-7,8-dihydroxybenzo(a)pyrene 9,10-oxide	increases expression	1
Gold Compounds	decreases expression	1
Sodium Selenite	decreases expression	1
Copper Sulfate	affects expression	1
Lactic Acid	decreases expression	1

Clinical trials (associated diseases)

Via MONDO — disease-level, not drug-specific.

showing 60 of 210 trials:

NCT	Phase	Status	Title
NCT04586348	Phase 4	UNKNOWN	Prenatal Iodine Supplementation and Early Childhood Neurodevelopment
NCT04873115	Phase 4	UNKNOWN	Double-blind, Placebo-controlled, Randomized Clinical Trial Comparing the Efficacy and Safety of Sialanar Plus orAl rehabiLitation Against Placebo Plus Oral Rehabilitation for chIldren and Adolescents With seVere Sialorrhoea and Neurodisabilties,
NCT02559102	Phase 3	COMPLETED	Dexmedetomidine Sedation Versus General Anaesthesia for Inguinal Hernia Surgery in Infants
NCT02757079	Phase 3	COMPLETED	Study of the Efficacy and Safety of NPC-15 for Sleep Disorders of Children With Neurodevelopmental Disorders
NCT06915480	Phase 3	RECRUITING	Reducing Missed Appointments
NCT07377032	Phase 3	RECRUITING	TAP-GRIN: Interventional Study on Patients With GRIN-related Neurodevelopmental Disorders
NCT02909959	Phase 2	COMPLETED	Sulforaphane for the Treatment of Young Men With Autism Spectrum Disorder
NCT06081348	Phase 2	RECRUITING	Sertraline vs. Placebo in the Treatment of Anxiety in Children and AdoLescents With NeurodevelopMental Disorders
NCT06352372	Phase 2	COMPLETED	Safety and Efficacy of tPBM for Epileptiform Activity in Autism
NCT00503191	Phase 1	COMPLETED	NeuroModulation Technique Treatment of Autism
NCT04475848	Phase 1	COMPLETED	A Study to Investigate the Safety, Tolerability, Pharmacokinetics, Pharmacodynamics and Food Effect of RO6953958 in Healthy Participants
NCT06300398	Phase 1	COMPLETED	IAMA-6 Oral Dose Study in Healthy Adults
NCT01783041	Phase 2/3	COMPLETED	Effect of Early L-Carnitine Supplementation on Neurodevelopmental Outcomes in Very Preterm Infants
NCT05767385	Phase 2/3	COMPLETED	Fetal Cerebrovascular Autoregulation in Congenital Heart Disease and Association With Neonatal Neurobehavior
NCT05675098	Early Phase 1	NOT_YET_RECRUITING	Central Nervous System Stimulants and Physical Function in Children With Cerebral Palsy
NCT00783783	Not specified	COMPLETED	CYP2D6 Pharmacogenetics in Risperidone-Treated Children
NCT01778504	Not specified	RECRUITING	Studying Childhood-onset Behavioral, Psychiatric, and Developmental Disorders
NCT01850784	Not specified	UNKNOWN	High Energy Formula Feeding in Infants With Congenital Heart Disease
NCT01922791	Not specified	COMPLETED	Nutrition and Pregnancy Intervention Study
NCT01942525	Not specified	UNKNOWN	Influence of Intrauterine Growth Restriction on Amplitude-integrated EEG in Preterm Infants
NCT02003170	Not specified	COMPLETED	Etiology and Early Diagnosis of Neurodevelopmental Disorders
NCT02118649	Not specified	COMPLETED	Enhancing Behavior and Brain Response to Visual Targets Using a Computer Game
NCT02557191	Not specified	TERMINATED	Biomarkers, Neurodevelopment and Preterm Infants
NCT02690675	Not specified	COMPLETED	Iron Supplement Effect on Child Development
NCT02694003	Not specified	COMPLETED	Better Nights, Better Days for Children With Neurodevelopment Disorders
NCT02792894	Not specified	COMPLETED	Family Networks (FaNs) for Children With Developmental Disorders and Delays
NCT02871674	Not specified	UNKNOWN	Good Night Project: Behavioural Sleep Interventions for Children With ADHD: A Randomised Controlled Trial
NCT02887157	Not specified	COMPLETED	Analyzing Retinal Microanatomy in ROP
NCT02898298	Not specified	COMPLETED	Positive Emotion Regulation Training in Children, Adolescents and Young Adults With and Without Developmental Disorder
NCT02912780	Not specified	UNKNOWN	Introduction of Microsystems in a Level 3 Neonatal Intensive Care Unit
NCT03023293	Not specified	COMPLETED	n-3 PUFAs, Irisin and Maternal Glucose Metabolism From Pregnancy to Postpartum
NCT03023644	Not specified	COMPLETED	Improving Neurodevelopmental Outcomes in Children With Congenital Heart Disease: An Intervention Study
NCT03032991	Not specified	UNKNOWN	Early Biomarkers of Neurodevelopment in Offspring of Diabetic Mothers
NCT03088189	Not specified	TERMINATED	Effect of Parental Peri-conceptional Vitamin B12 Supplementation on Infant Neurocognitive Development in Offspring
NCT03096028	Not specified	COMPLETED	Developmental Origins of Mental Health Disorders
NCT03148782	Not specified	COMPLETED	Brain Plasticity Underlying Acquisition of New Organizational Skills in Children-R61 Phase
NCT03172104	Not specified	COMPLETED	Neurobehavioural Development of Infants Born <30 Weeks Gestational Age Between Birth and Five Years of Age
NCT03222375	Not specified	RECRUITING	SQUED™ Series 28.1 Home-use and Treatment of Autowave Reverberator of Autism
NCT03229928	Not specified	COMPLETED	Clinical Testing of a Real-Time Behavior Measurement Tool: Measuring Outcomes for CHAnge
NCT03232489	Not specified	UNKNOWN	Study for the Evaluation of the Feasibility of Applying Advanced MRI Scanning in Pediatric Clinical Practice
NCT03381027	Not specified	COMPLETED	BABY SMART (Study of Massage Therapy, Sleep And neurodevelopMenT)
NCT03388294	Not specified	COMPLETED	Evaluation of a Novel Intervention for Infants At Risk for Neurodevelopmental Disorders
NCT03410810	Not specified	UNKNOWN	Childhood Outcomes of Preterm Brain Abnormalities
NCT03492060	Not specified	RECRUITING	Longitudinal Study of Neurogenetic Disorders
NCT03577756	Not specified	COMPLETED	Neurodevelopmental Assessment of Infants With Cystic Fibrosis
NCT03654248	Not specified	COMPLETED	Let’s Get Organized in Adult Psychiatric/habilitation Care
NCT03659279	Not specified	COMPLETED	Let’s Get Organized Feasibility Study
NCT03722615	Not specified	COMPLETED	Epidemiology of Congenital Cytomegalovirus in a High HIV Prevalence Setting, South Africa
NCT03770832	Not specified	ACTIVE_NOT_RECRUITING	Wearable Sensors and Video Recordings to Monitor Motor Development
NCT03830879	Not specified	RECRUITING	Shenzhen Birth Cohort Study
NCT03835689	Not specified	COMPLETED	Strongest FamiliesTM Neurodevelopmental
NCT03882788	Not specified	COMPLETED	The Effect of Anesthesia on Neurodevelopmental Outcome (NDO)
NCT03922087	Not specified	COMPLETED	No-worry Baby Project
NCT03977259	Not specified	ACTIVE_NOT_RECRUITING	Targeting Human Milk Fortification to Improve Preterm Infant Growth and Brain Development
NCT04043572	Not specified	UNKNOWN	The Biomarkers of Neurological Disease in Utero Study
NCT04096430	Not specified	RECRUITING	Evaluation of Effectiveness of Child-oriented Goal-setting in Paediatric Rehabilitation (the ENGAGE Approach)
NCT04108273	Not specified	COMPLETED	Brain Plasticity Underlying Acquisition of New Organizational Skills in Children
NCT04201509	Not specified	COMPLETED	Validity of Neurocognitive Assessment Methods in Childhood ADHD
NCT04233775	Not specified	UNKNOWN	Altered Cerebral Growth and Development in Infants With Congenital Heart Disease
NCT04313283	Not specified	COMPLETED	Translating Peer-to-Peer Support Into a Clinical Setting