ZMYND19

Summary

ZMYND19 (zinc finger MYND-type containing 19, HGNC:21146) is a protein-coding gene on chromosome 9q34.3, encoding Zinc finger MYND domain-containing protein 19 (Q96E35). May be involved as a regulatory molecule in GPR24/MCH-R1 signaling.

ZMYND19 is a MYND zinc finger domain-containing protein that binds to the C terminus of melanin-concentrating hormone receptor-1 (MCHR1; MIM 601751) (Bachner et al., 2002 [PubMed 12208518]), and to the N termini of alpha-tubulin (TUBA1; MIM 191110), and beta-tubulin (TUBB; MIM 191130) (Francke et al., 2005 [PubMed 16039987]).

Source: NCBI Gene 116225 — RefSeq curated summary.

At a glance

• GWAS associations: 3
• Clinical variants (ClinVar): 35 total — 1 likely-pathogenic
• MANE Select transcript: NM_138462

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:21146
Approved symbol	ZMYND19
Name	zinc finger MYND-type containing 19
Location	9q34.3
Locus type	gene with protein product
Status	Approved
Aliases	MIZIP
Ensembl gene	ENSG00000165724
Ensembl biotype	protein_coding
OMIM	611424
Entrez	116225

Gene structure

Transcript identifiers

Ensembl transcripts: 5 — 4 protein_coding, 1 protein_coding_CDS_not_defined

ENST00000298585, ENST00000471957, ENST00000923514, ENST00000942290, ENST00000942291

RefSeq mRNA: 1 — MANE Select: NM_138462 NM_138462

CCDS: CCDS7048

Canonical transcript exons

ENST00000298585 — 6 exons

Exon	Start	End
ENSE00001095856	137582081	137582686
ENSE00001120759	137582983	137583163
ENSE00001120767	137586967	137587107
ENSE00001120774	137587717	137587823
ENSE00001120778	137588659	137588718
ENSE00001300681	137590213	137590512

Expression profiles

Bgee: expression breadth ubiquitous, 236 present calls, max score 93.56.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 19.3383 / max 168.8527, expressed in 1774 samples.

FANTOM5 promoters (1 alternative TSS)

Promoter ID	TPM avg	Samples expressed
103384	19.3383	1774

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
left testis	UBERON:0004533	93.56	gold quality
right testis	UBERON:0004534	93.52	gold quality
testis	UBERON:0000473	91.66	gold quality
lower esophagus mucosa	UBERON:0035834	91.10	gold quality
body of stomach	UBERON:0001161	89.20	gold quality
cortical plate	UBERON:0005343	89.19	gold quality
skin of leg	UBERON:0001511	89.07	gold quality
skin of abdomen	UBERON:0001416	88.71	gold quality
esophagus mucosa	UBERON:0002469	88.35	gold quality
mucosa of transverse colon	UBERON:0004991	87.73	gold quality
prefrontal cortex	UBERON:0000451	87.42	gold quality
apex of heart	UBERON:0002098	87.31	gold quality
metanephros cortex	UBERON:0010533	87.30	gold quality
right frontal lobe	UBERON:0002810	87.10	gold quality
zone of skin	UBERON:0000014	87.01	gold quality
right hemisphere of cerebellum	UBERON:0014890	86.92	gold quality
embryo	UBERON:0000922	86.68	gold quality
ganglionic eminence	UBERON:0004023	86.68	gold quality
adenohypophysis	UBERON:0002196	86.67	gold quality
anterior cingulate cortex	UBERON:0009835	86.64	gold quality
Brodmann (1909) area 9	UBERON:0013540	86.59	gold quality
granulocyte	CL:0000094	86.58	gold quality
cerebellar hemisphere	UBERON:0002245	86.55	gold quality
stomach	UBERON:0000945	86.48	gold quality
cerebellar cortex	UBERON:0002129	86.41	gold quality
putamen	UBERON:0001874	86.35	gold quality
right adrenal gland cortex	UBERON:0035827	86.12	gold quality
right lobe of liver	UBERON:0001114	86.04	gold quality
caudate nucleus	UBERON:0001873	85.92	gold quality
minor salivary gland	UBERON:0001830	85.90	gold quality

Single-cell (SCXA)

Detected in 3 experiment(s), a significant marker in 2.

Experiment	Marker?	Max mean expression
E-GEOD-137537	yes	1452.03
E-ANND-3	yes	3.69
E-CURD-10	no	51.06

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

43 targeting ZMYND19, 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-5692A	100.00	74.40	6850
HSA-MIR-4776-3P	100.00	68.73	1340
HSA-MIR-4803	99.98	71.99	3117
HSA-MIR-520D-5P	99.98	73.34	4883
HSA-MIR-524-5P	99.98	73.43	4882
HSA-MIR-302C-5P	99.97	72.56	3642
HSA-MIR-6778-3P	99.96	67.29	2693
HSA-MIR-548AJ-3P	99.96	73.38	5345
HSA-MIR-548X-3P	99.96	73.38	5345
HSA-MIR-493-5P	99.96	72.47	2382
HSA-MIR-545-3P	99.95	70.74	2783
HSA-MIR-96-5P	99.95	72.80	2140
HSA-MIR-548J-3P	99.94	72.61	4881
HSA-MIR-548AE-3P	99.93	72.66	4867
HSA-MIR-548AH-3P	99.93	72.54	4872
HSA-MIR-548AM-3P	99.93	72.54	4872
HSA-MIR-548AQ-3P	99.93	72.66	4867
HSA-MIR-3143	99.93	71.96	3104
HSA-MIR-12133	99.92	71.82	2006
HSA-MIR-1271-5P	99.91	71.99	1972
HSA-MIR-548AR-3P	99.85	71.26	3889
HSA-MIR-548AZ-3P	99.82	70.56	3549
HSA-MIR-548BC	99.82	70.61	3524
HSA-MIR-548E-3P	99.82	70.59	3514
HSA-MIR-548F-3P	99.82	70.59	3540
HSA-MIR-548A-3P	99.76	70.58	3524
HSA-MIR-3120-3P	99.54	70.28	2669
HSA-MIR-548G-3P	99.48	68.67	2159
HSA-MIR-3692-5P	99.29	67.04	1421
HSA-MIR-4477B	99.23	70.49	1733

Literature-anchored findings (GeneRIF, showing 2)

• was identified from human brain and interacts with the C-terminus of melanin-concentrating hormone receptor 1 (PMID:12208518)
• Our results suggest that MIZIP might play an important role in mammalian cells by associating with tubulin and thus might provide a link between MCHR1 and tubulin functions. (PMID:16039987)

Cross-species orthologs

4 orthologs

Organism	Symbol	Gene ID
danio_rerio	zmynd19	ENSDARG00000100773
mus_musculus	Zmynd19	ENSMUSG00000026974
rattus_norvegicus	Zmynd19	ENSRNOG00000007752
drosophila_melanogaster	Zmynd10	FBGN0266709

Paralogs (2): ZMYND10 (ENSG00000004838), MSS51 (ENSG00000166343)

Protein

Protein identifiers

Zinc finger MYND domain-containing protein 19 — Q96E35 (reviewed: Q96E35)

Alternative names: Melanin-concentrating hormone receptor 1-interacting zinc finger protein

All UniProt accessions (1): Q96E35

UniProt curated annotations — full annotation on UniProt →

Function. May be involved as a regulatory molecule in GPR24/MCH-R1 signaling.

Subunit / interactions. Interacts with GPR24/MCH-R1.

Subcellular location. Cytoplasm. Cell membrane.

Tissue specificity. Expressed in brain, testis, placenta, heart, liver, skeletal muscle, kidney and stomach.

RefSeq proteins (1): NP_612471* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR002893	Znf_MYND	Domain
IPR003615	HNH_nuc	Domain
IPR032978	ZMYND19	Family
IPR044925	His-Me_finger_sf	Homologous_superfamily

Pfam: PF01753, PF13392

UniProt features (6 total): binding site 4, chain 1, zinc finger region 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q96E35-F1	83.80	0.52

Functional residue map

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

Ligand- & substrate-binding residues (4): 187; 190; 208; 212

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 87 (showing top): RODRIGUES_THYROID_CARCINOMA_ANAPLASTIC_UP, FISCHER_G1_S_CELL_CYCLE, ATGTTAA_MIR302C, MONNIER_POSTRADIATION_TUMOR_ESCAPE_UP, WEI_MYCN_TARGETS_WITH_E_BOX, LIAO_METASTASIS, FISCHER_DREAM_TARGETS, DOUGLAS_BMI1_TARGETS_UP, GINESTIER_BREAST_CANCER_ZNF217_AMPLIFIED_DN, ATGTACA_MIR493, GOCC_SYNAPSE, MARSON_BOUND_BY_E2F4_UNSTIMULATED, SANSOM_APC_MYC_TARGETS, SANSOM_APC_TARGETS_REQUIRE_MYC, KRIGE_RESPONSE_TO_TOSEDOSTAT_6HR_DN

GO Biological Process (0):

GO Molecular Function (3): zinc ion binding (GO:0008270), protein binding (GO:0005515), metal ion binding (GO:0046872)

GO Cellular Component (4): cytoplasm (GO:0005737), plasma membrane (GO:0005886), membrane (GO:0016020), synapse (GO:0045202)

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
cellular anatomical structure	2
transition metal ion binding	1
binding	1
cation binding	1
intracellular anatomical structure	1
membrane	1
cell periphery	1
cell junction	1

Protein interactions and networks

STRING

752 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
ZMYND19	FAM170A	A1A519	826
ZMYND19	DEAF1	O75398	810
ZMYND19	MCHR1	Q99705	779
ZMYND19	TUBA4A	P05215	750
ZMYND19	TUBB2A	Q13885	639
ZMYND19	TUBB	P05218	634
ZMYND19	ARMC8	Q8IUR7	607
ZMYND19	HTRA2	O43464	576
ZMYND19	RUNX1T1	Q06455	547
ZMYND19	MAEA	Q7L5Y9	540
ZMYND19	RMND5A	Q9H871	509
ZMYND19	PLEKHJ1	Q9NW61	445
ZMYND19	TTC14	Q96N46	439
ZMYND19	TMEM168	Q9H0V1	431
ZMYND19	CCDC28A	Q8IWP9	430

IntAct

289 interactions, top by confidence:

A	B	Type	Score
HACL1	ZMYND19	psi-mi:“MI:0915”(physical association)	0.830
ZMYND19	HACL1	psi-mi:“MI:0915”(physical association)	0.830
ZMYND19	NAB2	psi-mi:“MI:0915”(physical association)	0.780
KCTD13	ZMYND19	psi-mi:“MI:0915”(physical association)	0.780
ZMYND19	KCTD13	psi-mi:“MI:0915”(physical association)	0.780
NAB2	ZMYND19	psi-mi:“MI:0915”(physical association)	0.780
SELENOV	ZMYND19	psi-mi:“MI:0915”(physical association)	0.720
ZMYND19	SAXO1	psi-mi:“MI:0915”(physical association)	0.720
TOX4	ZMYND19	psi-mi:“MI:0915”(physical association)	0.720
ZMYND19	ENOX1	psi-mi:“MI:0915”(physical association)	0.720
PNMA5	ZMYND19	psi-mi:“MI:0915”(physical association)	0.720
ZMYND19	SELENOV	psi-mi:“MI:0915”(physical association)	0.720
SAXO1	ZMYND19	psi-mi:“MI:0915”(physical association)	0.720
ZMYND19	PNMA5	psi-mi:“MI:0915”(physical association)	0.720
ENOX1	ZMYND19	psi-mi:“MI:0915”(physical association)	0.720

BioGRID (170): ZMYND19 (Two-hybrid), ZMYND19 (Two-hybrid), ZMYND19 (Two-hybrid), ZMYND19 (Two-hybrid), ZMYND19 (Two-hybrid), ZMYND19 (Two-hybrid), ZMYND19 (Two-hybrid), ZMYND19 (Two-hybrid), FAM154A (Two-hybrid), KCTD13 (Two-hybrid), SELV (Two-hybrid), INCA1 (Two-hybrid), CCDC183 (Affinity Capture-MS), ZMYND19 (Affinity Capture-MS), ZMYND19 (Affinity Capture-MS)

ESM2 similar proteins: A2VDK9, A3KN28, A5PK00, A8C8W3, A9JRA0, O04300, O22666, O43513, P03455, P0A4M1, P0A4M2, P0C0A2, P11497, P26140, P29010, P33790, P61008, P61009, P76512, Q05B58, Q108U3, Q13085, Q28559, Q28GR4, Q2F7Z4, Q2QL86, Q2TBU2, Q3SZU5, Q3T123, Q3ZAQ7, Q5RDV3, Q5RF53, Q5SWU9, Q6ZWQ7, Q78T54, Q86VN1, Q8H8T0, Q8RU27, Q8X5L8, Q91XD6

Diamond homologs: A9CPT4, C3RZA1, D3ZKV9, E1C5V0, F1QN74, F1RET2, O74467, P97443, Q0P585, Q12529, Q3TYX3, Q4VC12, Q5BJI7, Q5F3V0, Q5R5X9, Q5RGL7, Q5UNT8, Q5ZIZ2, Q6C9E7, Q6GMV2, Q6GN68, Q6GPQ4, Q7M6Z3, Q7TSV3, Q7ZXV5, Q8BTK5, Q8IYR2, Q8NB12, Q8R5A0, Q91YE3, Q96E35, Q9BXT4, Q9CQG3, Q9CWR2, Q9D5Z5, Q9GZT9, Q9H7B4, Q9N3Q8, Q9NRG4, A3M0J3

SIGNOR signaling

0 interactions.

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 90 IntAct physical interaction partners (hypergeometric vs the genome-wide background, BH-FDR, gene-set size 15–500, ranked by fold). A functional readout of the neighbourhood — distinct from this gene’s own memberships above, and biased toward well-studied / hub proteins, so read it as themes rather than proof.

Reactome pathways:

Pathway	Partners	Fold	FDR
Aerobic respiration and respiratory electron transport	6	10.0×	5e-03

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	1
Uncertain significance	24
Likely benign	0
Benign	3

Top pathogenic / likely-pathogenic (1)

Variant ID	HGVS	Classification
2576633	GRCh37/hg19 9q34.3(chr9:140233379-140756825)x3	Likely pathogenic

SpliceAI

1025 predictions. Top by Δscore:

Variant	Effect	Δscore
9:137582978:CCCA:C	donor_loss	1.0000
9:137582979:CCA:C	donor_loss	1.0000
9:137582980:CA:C	donor_loss	1.0000
9:137582981:A:AT	donor_loss	1.0000
9:137582982:C:CG	donor_loss	1.0000
9:137582982:CCTG:C	donor_gain	1.0000
9:137583162:CC:C	acceptor_gain	1.0000
9:137583163:CCT:C	acceptor_gain	1.0000
9:137583164:C:T	acceptor_gain	1.0000
9:137583165:T:C	acceptor_gain	1.0000
9:137586966:CCT:C	donor_gain	1.0000
9:137587752:T:A	donor_gain	1.0000
9:137587819:CGGGC:C	acceptor_gain	1.0000
9:137587822:GCC:G	acceptor_loss	1.0000
9:137587824:C:CC	acceptor_gain	1.0000
9:137587825:T:C	acceptor_loss	1.0000
9:137588656:TACCT:T	donor_loss	1.0000
9:137588657:A:AC	donor_gain	1.0000
9:137588657:AC:A	donor_gain	1.0000
9:137588657:ACC:A	donor_loss	1.0000
9:137588658:C:CA	donor_gain	1.0000
9:137588658:CC:C	donor_gain	1.0000
9:137588658:CCT:C	donor_gain	1.0000
9:137583023:T:C	donor_gain	0.9900
9:137583044:T:TA	donor_gain	0.9900
9:137583160:CTCC:C	acceptor_gain	0.9900
9:137583161:TCCCT:T	acceptor_loss	0.9900
9:137583162:CCCT:C	acceptor_gain	0.9900
9:137583164:C:CA	acceptor_loss	0.9900
9:137583164:C:CC	acceptor_gain	0.9900

AlphaMissense

1483 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
9:137582593:A:G	C212R	1.000
9:137582612:C:A	W205C	1.000
9:137582612:C:G	W205C	1.000
9:137582614:A:G	W205R	1.000
9:137582614:A:T	W205R	1.000
9:137582628:C:G	C200S	1.000
9:137582629:A:G	C200R	1.000
9:137582629:A:T	C200S	1.000
9:137582641:A:G	C196R	1.000
9:137582644:A:C	Y195D	1.000
9:137582644:A:G	Y195H	1.000
9:137582657:G:C	C190W	1.000
9:137582658:C:A	C190F	1.000
9:137582658:C:G	C190S	1.000
9:137582658:C:T	C190Y	1.000
9:137582659:A:G	C190R	1.000
9:137582659:A:T	C190S	1.000
9:137582666:A:C	C187W	1.000
9:137582667:C:G	C187S	1.000
9:137582667:C:T	C187Y	1.000
9:137582668:A:G	C187R	1.000
9:137582668:A:T	C187S	1.000
9:137582675:G:C	F184L	1.000
9:137582675:G:T	F184L	1.000
9:137582676:A:G	F184S	1.000
9:137582677:A:G	F184L	1.000
9:137583003:A:G	C174R	1.000
9:137583016:G:C	C169W	1.000
9:137583017:C:G	C169S	1.000
9:137583017:C:T	C169Y	1.000

dbSNP variants (sampled 300 via entrez): RS1000365012 (9:137591083 C>G,T), RS1000438762 (9:137591364 C>G,T), RS1000458971 (9:137584274 T>C,G), RS1000617867 (9:137588472 G>C,T), RS1000697740 (9:137590491 C>A,T), RS1001167594 (9:137591694 G>A,C), RS1001184242 (9:137586936 G>A), RS1001354888 (9:137586403 G>C), RS1001398121 (9:137581990 C>T), RS1001426463 (9:137587216 G>A), RS1001651184 (9:137590856 C>T), RS1001767621 (9:137581727 G>A,C), RS1001870632 (9:137591928 G>A,C), RS1001900751 (9:137582909 G>A,C), RS1001928888 (9:137587540 G>A)

Disease associations

OMIM: gene MIM:611424 | 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
GCST007267_194	Systolic blood pressure	1.000000e-08
GCST007994_19	Asthma (age of onset)	3.000000e-08
GCST007995_55	Asthma (childhood onset)	4.000000e-09

EFO canonical traits (1, from GWAS)

EFO ID	Trait name
EFO:0006335	systolic blood pressure

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

22 total (human), top 22 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
Cadmium Chloride	decreases expression, increases expression	3
Acetaminophen	increases expression, decreases expression	2
Tretinoin	decreases expression, increases expression	2
7,8-Dihydro-7,8-dihydroxybenzo(a)pyrene 9,10-oxide	decreases expression	2
sodium arsenite	decreases expression	1
beta-methylcholine	affects expression	1
di-n-butylphosphoric acid	affects expression	1
abrine	decreases expression	1
2-(1H-indazol-4-yl)-6-(4-methanesulfonylpiperazin-1-ylmethyl)-4-morpholin-4-ylthieno(3,2-d)pyrimidine	decreases expression, increases response to substance	1
NSC 689534	affects binding, decreases expression	1
Temozolomide	increases expression	1
Sunitinib	increases expression	1
Arsenic	affects methylation	1
Cadmium	decreases expression	1
Copper	affects binding, decreases expression	1
Formaldehyde	decreases expression	1
Silicon Dioxide	increases expression	1
Smoke	decreases expression	1
Thiram	decreases expression	1
Tobacco Smoke Pollution	increases expression	1
Aflatoxin B1	increases expression	1
tert-Butylhydroperoxide	increases methylation	1

Clinical trials (associated diseases)

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