INAFM1

Summary

INAFM1 (InaF motif containing 1, HGNC:27406) is a protein-coding gene on chromosome 19q13.32, encoding Putative transmembrane protein INAFM1 (C9JVW0).

Predicted to be located in membrane.

Source: NCBI Gene 255783 — RefSeq curated summary.

At a glance

• Clinical variants (ClinVar): 5 total — 1 likely-pathogenic
• MANE Select transcript: NM_178511

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:27406
Approved symbol	INAFM1
Name	InaF motif containing 1
Location	19q13.32
Locus type	gene with protein product
Status	Approved
Ensembl gene	ENSG00000257704
Ensembl biotype	protein_coding
Entrez	255783

Gene structure

Transcript identifiers

Ensembl transcripts: 2 — 1 protein_coding, 1 protein_coding_CDS_not_defined

ENST00000552360, ENST00000851061

RefSeq mRNA: 1 — MANE Select: NM_178511 NM_178511

CCDS: CCDS46131

Canonical transcript exons

ENST00000552360 — 1 exons

Exon	Start	End
ENSE00004283604	47274885	47275723

Expression profiles

Bgee: expression breadth ubiquitous, 251 present calls, max score 97.96.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 14.0775 / max 189.8923, expressed in 1762 samples.

FANTOM5 promoters (4 alternative TSS)

Promoter ID	TPM avg	Samples expressed
176651	5.5097	1087
176650	4.4054	1434
176653	2.7628	1221
176652	1.3996	419

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
decidua	UBERON:0002450	97.96	gold quality
left adrenal gland cortex	UBERON:0035825	96.53	gold quality
left adrenal gland	UBERON:0001234	96.38	gold quality
right adrenal gland	UBERON:0001233	96.20	gold quality
adrenal cortex	UBERON:0001235	96.06	gold quality
cardiac muscle of right atrium	UBERON:0003379	95.56	gold quality
right adrenal gland cortex	UBERON:0035827	95.06	gold quality
popliteal artery	UBERON:0002250	93.82	gold quality
tibial artery	UBERON:0007610	93.82	gold quality
apex of heart	UBERON:0002098	93.57	gold quality
left uterine tube	UBERON:0001303	93.39	gold quality
endocervix	UBERON:0000458	93.30	gold quality
kidney epithelium	UBERON:0004819	93.21	gold quality
aorta	UBERON:0000947	93.19	gold quality
body of uterus	UBERON:0009853	93.06	gold quality
right ovary	UBERON:0002118	93.01	gold quality
right coronary artery	UBERON:0001625	92.98	gold quality
muscle layer of sigmoid colon	UBERON:0035805	92.94	gold quality
adrenal gland	UBERON:0002369	92.81	gold quality
left ventricle myocardium	UBERON:0006566	92.67	gold quality
ascending aorta	UBERON:0001496	92.44	gold quality
thoracic aorta	UBERON:0001515	92.40	gold quality
descending thoracic aorta	UBERON:0002345	92.37	gold quality
coronary artery	UBERON:0001621	92.34	gold quality
left coronary artery	UBERON:0001626	92.19	gold quality
left ovary	UBERON:0002119	92.07	gold quality
upper arm skin	UBERON:0004263	92.01	gold quality
ectocervix	UBERON:0012249	92.00	gold quality
esophagogastric junction muscularis propria	UBERON:0035841	91.91	gold quality
lower esophagus muscularis layer	UBERON:0035833	91.83	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-MTAB-6701	yes	118.96
E-MTAB-8410	yes	16.62
E-ANND-3	yes	8.78

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

23 targeting INAFM1, 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-6851-5P	100.00	65.63	1294
HSA-MIR-32-5P	99.98	75.21	1964
HSA-MIR-92A-3P	99.98	75.21	1960
HSA-MIR-92B-3P	99.98	75.25	1955
HSA-MIR-25-3P	99.98	74.60	1817
HSA-MIR-363-3P	99.98	74.72	1821
HSA-MIR-367-3P	99.98	74.83	1819
HSA-MIR-137-3P	99.87	74.74	2401
HSA-MIR-4492	99.87	68.25	3611
HSA-MIR-3934-3P	99.76	65.51	1351
HSA-MIR-1827	99.63	68.57	3265
HSA-MIR-4441	99.49	66.56	3216
HSA-MIR-520A-5P	99.35	66.72	1632
HSA-MIR-525-5P	99.35	66.85	1615
HSA-MIR-7854-3P	99.08	66.26	1117
HSA-MIR-4270	99.02	66.26	1987
HSA-MIR-6754-5P	98.60	65.54	1627
HSA-MIR-6819-5P	97.96	66.59	1071
HSA-MIR-6737-5P	97.75	66.54	1044
HSA-MIR-6812-5P	97.56	65.39	1059
HSA-MIR-12128	96.67	66.98	1471
HSA-MIR-4296	96.35	63.55	1233
HSA-MIR-324-5P	95.68	65.20	560

Cross-species orthologs

1 orthologs

Organism	Symbol	Gene ID
mus_musculus	Inafm1	ENSMUSG00000091811

Protein

Protein identifiers

Putative transmembrane protein INAFM1 — C9JVW0 (reviewed: C9JVW0)

Alternative names: InaF-motif-containing protein 1, Proline-rich protein 24

All UniProt accessions (1): C9JVW0

UniProt curated annotations — full annotation on UniProt →

Subcellular location. Membrane.

RefSeq proteins (1): NP_848606* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR029162	InaF-motif	Conserved_site

Pfam: PF15018

UniProt features (9 total): compositionally biased region 4, region of interest 3, chain 1, transmembrane region 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-C9JVW0-F1	60.01	0.11

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 42 (showing top): KRIGE_RESPONSE_TO_TOSEDOSTAT_24HR_UP, BRUINS_UVC_RESPONSE_VIA_TP53_GROUP_D, LEE_BMP2_TARGETS_UP, CHAF1B_TARGET_GENES, ZBTB12_TARGET_GENES, ZNF184_TARGET_GENES, GSE10094_LCMV_VS_LISTERIA_IND_EFF_CD4_TCELL_UP, GSE14769_UNSTIM_VS_360MIN_LPS_BMDM_UP, FAN_EMBRYONIC_CTX_BIG_GROUPS_CAJAL_RETZIUS, THAKAR_PBMC_INACTIVATED_INFLUENZA_AGE_21_30YO_RESPONDERS_7DY_DN, HARALAMBIEVA_PBMC_M_M_R_II_AGE_11_22YO_VACCINATED_VS_UNVACCINATED_7YR_UP, OSMAN_BLOOD_CHAD63_KH_AGE_18_50YO_HIGH_DOSE_SUBJECTS_24HR_UP, GSE18791_CTRL_VS_NEWCASTLE_VIRUS_DC_18H_DN, GSE18791_UNSTIM_VS_NEWCATSLE_VIRUS_DC_18H_DN, GSE20366_CD103_POS_VS_CD103_KLRG1_DP_TREG_UP

GO Biological Process (0):

GO Molecular Function (0):

GO Cellular Component (1): membrane (GO:0016020)

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
cellular anatomical structure	1

Protein interactions and networks

STRING

144 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
INAFM1	DIP2C-AS1	Q8N8Z3	507
INAFM1	AFTPH	Q6ULP2	464
INAFM1	TBC1D22B	Q9NU19	454
INAFM1	ZNF628	Q5EBL2	447
INAFM1	UBALD1	Q8TB05	446
INAFM1	ZBTB45	Q96K62	432
INAFM1	SFT2D2	O95562	410
INAFM1	RPUSD1	Q9UJJ7	407
INAFM1	PRR12	Q9ULL5	404
INAFM1	EPM2AIP1	Q7L775	377
INAFM1	CAPN15	O75808	374
INAFM1	TMEM259	Q4ZIN3	370
INAFM1	PNO1	Q9NRX1	365
INAFM1	TMEM100	Q9NV29	365
INAFM1	TIPRL	O75663	360

IntAct

0 interactions, top by confidence:

BioGRID (1): INAFM1 (Affinity Capture-RNA)

ESM2 similar proteins: A0A0U1RQ45, A0A0U1RQS6, A0A286YF58, A0A2R8YCJ5, A0A7I2V3R4, A2A699, A2VDX9, A6NCS6, A6NGB7, A6NJG2, A6NKF7, A6NKL6, A6NLJ0, A8MVW0, B2RU40, B7Z1M9, B8ZZ34, C9JH25, C9JVW0, D4A9R4, J3QNX5, M0QZC1, P03971, P0CG09, P0DPE3, Q0PHV7, Q0VD38, Q14761, Q29RK8, Q29RM6, Q2KJ18, Q2M3G4, Q2M3V2, Q5T442, Q64697, Q69YZ2, Q6F5E0, Q6NY19, Q6UXK2, Q80XF7

Diamond homologs: C9JVW0, P0DMQ5

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	1
Uncertain significance	4
Likely benign	0
Benign	0

Top pathogenic / likely-pathogenic (1)

Variant ID	HGVS	Classification
2504578	GRCh37/hg19 19q13.32-13.33(chr19:47028919-48185409)	Likely pathogenic

SpliceAI

203 predictions. Top by Δscore:

Variant	Effect	Δscore
19:47274507:G:GG	donor_gain	0.9500
19:47274504:GAA:G	donor_gain	0.9200
19:47274663:G:GA	donor_gain	0.9000
19:47274621:G:T	donor_gain	0.8900
19:47274506:A:AG	donor_gain	0.8700
19:47274621:G:GT	donor_gain	0.8600
19:47274535:T:A	donor_gain	0.8200
19:47274662:T:TA	donor_gain	0.8100
19:47274646:G:GT	donor_gain	0.7900
19:47274511:G:GT	donor_gain	0.7800
19:47275045:A:AG	acceptor_gain	0.7700
19:47275046:G:GG	acceptor_gain	0.7700
19:47275209:T:TA	acceptor_gain	0.7600
19:47274495:ACAG:A	donor_loss	0.7500
19:47274497:AGGTA:A	donor_loss	0.7500
19:47274498:GG:G	donor_loss	0.7500
19:47274499:G:T	donor_loss	0.7500
19:47274500:T:G	donor_loss	0.7500
19:47274642:G:GT	donor_gain	0.7500
19:47275210:G:A	acceptor_gain	0.7500
19:47274504:G:GT	donor_gain	0.7400
19:47274528:G:GT	donor_gain	0.7400
19:47274655:A:AG	donor_gain	0.7400
19:47274550:GGCT:G	donor_gain	0.7200
19:47274656:T:G	donor_gain	0.7100
19:47275104:C:CA	acceptor_gain	0.7100
19:47274547:C:T	donor_gain	0.7000
19:47275046:GCT:G	acceptor_gain	0.6900
19:47274512:A:T	donor_gain	0.6700
19:47274643:G:T	donor_gain	0.6700

AlphaMissense

866 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
19:47275034:T:C	C39R	0.997
19:47275059:T:A	L47H	0.997
19:47275050:C:A	A44D	0.995
19:47275019:T:C	C34R	0.994
19:47275025:T:C	Y36H	0.994
19:47275038:T:A	V40D	0.992
19:47275023:C:A	A35D	0.991
19:47275047:C:A	A43D	0.991
19:47275062:C:A	A48D	0.991
19:47275035:G:A	C39Y	0.989
19:47275084:G:C	W55C	0.988
19:47275084:G:T	W55C	0.988
19:47275067:T:C	Y50H	0.987
19:47275067:T:G	Y50D	0.986
19:47275073:G:C	G52R	0.986
19:47275074:G:A	G52D	0.985
19:47275011:C:A	A31D	0.984
19:47275032:T:A	L38H	0.983
19:47275056:T:G	L46R	0.983
19:47275059:T:G	L47R	0.983
19:47275025:T:G	Y36D	0.981
19:47275059:T:C	L47P	0.980
19:47275053:T:A	V45E	0.977
19:47275036:C:G	C39W	0.975
19:47275080:T:A	I54N	0.975
19:47275065:T:A	V49E	0.974
19:47275082:T:A	W55R	0.974
19:47275082:T:C	W55R	0.974
19:47275056:T:A	L46Q	0.973
19:47275070:T:C	Y51H	0.972

dbSNP variants (sampled 300 via entrez): RS1000820712 (19:47275085 G>A), RS1000936321 (19:47275179 C>A,T), RS1001696872 (19:47273166 T>C), RS1001992971 (19:47274064 C>A,T), RS1002369923 (19:47274470 T>G), RS1002379898 (19:47274282 C>A,T), RS1003152272 (19:47272591 C>G,T), RS1003371334 (19:47273594 C>T), RS1003381511 (19:47273443 C>T), RS1003486497 (19:47273820 G>A,T), RS1004774330 (19:47275423 G>A), RS1005494854 (19:47273427 G>A), RS1005705599 (19:47273829 C>G,T), RS1006114695 (19:47274477 C>G,T), RS1006838534 (19:47272742 G>C)

Disease associations

OMIM: gene `` | disease phenotypes: MIM:619325

GenCC curated gene-disease

Mondo (1): Coffin-Siris syndrome 12 (MONDO:0025699)

Orphanet (0):

HPO phenotypes

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

GWAS associations

0 associations (top):

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

19 total (human), top 19 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
Valproic Acid	affects expression, increases expression	5
Air Pollutants	affects methylation, increases abundance, affects expression, decreases expression	3
Particulate Matter	increases abundance, decreases expression, affects methylation	3
triphenyl phosphate	affects expression	1
sodium arsenite	increases expression	1
ICG 001	increases expression	1
abrine	increases expression	1
licochalcone B	increases expression	1
Sunitinib	decreases expression	1
Benzo(a)pyrene	affects methylation, increases methylation	1
Cisplatin	decreases expression	1
Methyl Methanesulfonate	increases expression	1
Niclosamide	increases expression	1
Nitrogen Dioxide	increases abundance, affects methylation	1
Ozone	affects expression, increases abundance	1
Quercetin	increases expression	1
Smoke	decreases expression	1
Thimerosal	decreases expression	1
Triclosan	increases expression	1

Clinical trials (associated diseases)

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