FAM153A

Summary

FAM153A (family with sequence similarity 153 member A, HGNC:29940) is a protein-coding gene on chromosome 5q35.3, encoding Protein FAM153A (Q9UHL3).

At a glance

• GWAS associations: 2
• Clinical variants (ClinVar): 36 total — 1 pathogenic
• MANE Select transcript: NM_001413826

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:29940
Approved symbol	FAM153A
Name	family with sequence similarity 153 member A
Location	5q35.3
Locus type	gene with protein product
Status	Approved
Aliases	NY-REN-7
Ensembl gene	ENSG00000170074
Ensembl biotype	protein_coding
Entrez	285596

Gene structure

Transcript identifiers

Ensembl transcripts: 39 — 15 protein_coding_CDS_not_defined, 12 nonsense_mediated_decay, 9 protein_coding, 3 retained_intron

ENST00000360669, ENST00000440605, ENST00000503136, ENST00000503567, ENST00000503845, ENST00000503909, ENST00000504518, ENST00000505683, ENST00000506011, ENST00000506229, ENST00000506354, ENST00000507615, ENST00000509607, ENST00000510276, ENST00000512544, ENST00000512612, ENST00000513363, ENST00000513554, ENST00000514899, ENST00000515787, ENST00000614127, ENST00000697103, ENST00000697104, ENST00000697105, ENST00000697106, ENST00000697107, ENST00000697108, ENST00000697109, ENST00000697110, ENST00000697111, ENST00000697112, ENST00000697113, ENST00000697114, ENST00000697115, ENST00000697116, ENST00000697117, ENST00000697118, ENST00000697119, ENST00000969383

RefSeq mRNA: 3 — MANE Select: NM_001413826 NM_001394339, NM_001413826, NM_173663

CCDS: CCDS34305, CCDS93833

Canonical transcript exons

ENST00000697116 — 23 exons

Exon	Start	End
ENSE00002069657	177741256	177741332
ENSE00002458775	177763317	177763510
ENSE00002517759	177780449	177780504
ENSE00003538775	177747769	177747793
ENSE00003602528	177744888	177744967
ENSE00003626709	177744394	177744418
ENSE00003673899	177748641	177748699
ENSE00003969519	177736579	177736609
ENSE00003969522	177737042	177737112
ENSE00003969523	177734380	177734404
ENSE00003969529	177739600	177739670
ENSE00003969538	177723364	177724206
ENSE00003969540	177740777	177740801
ENSE00003969555	177724784	177724821
ENSE00003969557	177739113	177739137
ENSE00003969559	177729023	177729053
ENSE00003969563	177734863	177734933
ENSE00003969568	177782743	177782899
ENSE00003969570	177731569	177731599
ENSE00003969571	177732030	177732100
ENSE00003969578	177767150	177767180
ENSE00003969583	177729485	177729555
ENSE00003969586	177724295	177724362

Expression profiles

Bgee: expression breadth ubiquitous, 131 present calls, max score 97.21.

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
right testis	UBERON:0004534	97.21	gold quality
left testis	UBERON:0004533	97.10	gold quality
testis	UBERON:0000473	95.60	gold quality
mucosa of stomach	UBERON:0001199	95.07	gold quality
cerebellar hemisphere	UBERON:0002245	93.96	gold quality
cerebellar cortex	UBERON:0002129	93.93	gold quality
cerebellum	UBERON:0002037	93.89	gold quality
right hemisphere of cerebellum	UBERON:0014890	93.87	gold quality
spleen	UBERON:0002106	92.63	gold quality
right uterine tube	UBERON:0001302	92.31	gold quality
superior frontal gyrus	UBERON:0002661	91.01	gold quality
pituitary gland	UBERON:0000007	90.58	gold quality
adenohypophysis	UBERON:0002196	90.48	gold quality
right frontal lobe	UBERON:0002810	90.39	gold quality
primary visual cortex	UBERON:0002436	89.94	gold quality
Brodmann (1909) area 9	UBERON:0013540	87.21	gold quality
dorsolateral prefrontal cortex	UBERON:0009834	87.15	gold quality
prostate gland	UBERON:0002367	87.01	gold quality
nucleus accumbens	UBERON:0001882	86.08	gold quality
anterior cingulate cortex	UBERON:0009835	85.17	gold quality
apex of heart	UBERON:0002098	85.12	gold quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	85.06	gold quality
brain	UBERON:0000955	83.99	gold quality
caudate nucleus	UBERON:0001873	83.19	gold quality
esophagogastric junction muscularis propria	UBERON:0035841	83.05	gold quality
Ammon’s horn	UBERON:0001954	82.96	gold quality
cerebral cortex	UBERON:0000956	82.57	gold quality
putamen	UBERON:0001874	82.55	gold quality
temporal lobe	UBERON:0001871	80.96	gold quality
amygdala	UBERON:0001876	80.92	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	no	5.62

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

26 targeting FAM153A, 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-1277-5P	100.00	73.95	5056
HSA-MIR-6798-5P	100.00	65.77	699
HSA-MIR-6783-3P	99.89	67.92	2059
HSA-MIR-1343-3P	99.89	66.78	1815
HSA-MIR-4492	99.87	68.25	3611
HSA-MIR-6842-5P	99.80	67.54	1587
HSA-MIR-7110-5P	99.80	67.84	1712
HSA-MIR-6762-3P	99.66	66.94	1188
HSA-MIR-520E-5P	99.27	68.90	1513
HSA-MIR-4254	99.11	65.15	1315
HSA-MIR-485-5P	99.10	64.78	1889
HSA-MIR-6884-5P	99.10	64.50	1987
HSA-MIR-3160-3P	99.07	64.78	955
HSA-MIR-6829-5P	98.86	65.12	1480
HSA-MIR-6852-3P	98.54	67.60	1468
HSA-MIR-3166	98.24	66.63	1223
HSA-MIR-6072	98.00	66.47	804
HSA-MIR-4469	97.93	65.81	1319
HSA-MIR-7106-3P	97.33	65.33	644
HSA-MIR-509-3-5P	97.21	67.74	1517
HSA-MIR-509-5P	97.21	67.90	1512
HSA-MIR-4418	97.04	67.16	1372
HSA-MIR-1291	96.28	65.89	1224
HSA-MIR-6891-3P	95.80	65.76	683
HSA-MIR-6775-3P	95.76	65.91	982
HSA-MIR-6851-3P	95.73	65.11	688

Cross-species orthologs

0 orthologs

Paralogs (1): (ENSG00000289731)

Protein

Protein identifiers

Protein FAM153A — Q9UHL3 (reviewed: Q9UHL3)

Alternative names: Renal carcinoma antigen NY-REN-7

All UniProt accessions (11): Q9UHL3, A0A087WYN1, A0A8V8TKN8, A0A8V8TKQ6, A0A8V8TL23, A0A8V8TLZ1, A0A8V8TM68, D6RCD4, D6RF32, D6RF64, D6RIF1

UniProt curated annotations — full annotation on UniProt →

Similarity. Belongs to the FAM153 family.

RefSeq proteins (3): NP_001381268, NP_001400755, NP_775934 (=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR023249	FAM153	Family

Pfam: PF15722

UniProt features (12 total): region of interest 4, sequence conflict 4, compositionally biased region 3, chain 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q9UHL3-F1	52.44	0.00

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 40 (showing top): WAMUNYOKOLI_OVARIAN_CANCER_LMP_DN, NAKAMURA_TUMOR_ZONE_PERIPHERAL_VS_CENTRAL_DN, SHEN_SMARCA2_TARGETS_DN, DODD_NASOPHARYNGEAL_CARCINOMA_DN, ZWANG_TRANSIENTLY_UP_BY_2ND_EGF_PULSE_ONLY, SRC_UP.V1_DN, PRC1_BMI_UP.V1_UP, CTIP_DN.V1_UP, KRAS.DF.V1_DN, GSE10463_CD40L_AND_VA347_VS_CD40L_IN_DC_DN, MIR1291, MIR6775_3P, MIR3160_3P, MEBARKI_HCC_PROGENITOR_FZD8CRD_DN, DESCARTES_FETAL_CEREBRUM_SKOR2_NPSR1_POSITIVE_CELLS

GO Biological Process (0):

GO Molecular Function (1): protein binding (GO:0005515)

GO Cellular Component (0):

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
binding	1

Protein interactions and networks

STRING

334 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
FAM153A	TRIM77	I1YAP6	480
FAM153A	SAMD15	Q9P1V8	472
FAM153A	CFAP77	Q6ZQR2	447
FAM153A	MTMR9	Q96QG7	371
FAM153A	TMED8	Q6PL24	370
FAM153A	ZNF396	Q96N95	358
FAM153A	MTMR8	Q96EF0	351
FAM153A	MNMIP1	A4FU49	326
FAM153A	ARMC12	Q5T9G4	324
FAM153A	SLC35G5	Q96KT7	324
FAM153A	CDC14C	A4D256	324
FAM153A	SWT1	Q5T5J6	323
FAM153A	CCDC177	Q9NQR7	323
FAM153A	SPINK13	Q1W4C9	317
FAM153A	LONRF1	Q17RB8	311

IntAct

12 interactions, top by confidence:

A	B	Type	Score
DYNLL1	FAM153A	psi-mi:“MI:0915”(physical association)	0.600
FAM153A	DYNLL1	psi-mi:“MI:0915”(physical association)	0.600
ROPN1	FAM153A	psi-mi:“MI:0915”(physical association)	0.560
FAM153B	TYW5	psi-mi:“MI:0914”(association)	0.350
FAM153A	ANKRD13D	psi-mi:“MI:0914”(association)	0.350
FAM153B	A2ML1	psi-mi:“MI:0914”(association)	0.350
FAM153A	ROPN1	psi-mi:“MI:0915”(physical association)	0.000
FAM153A	DYNLL1	psi-mi:“MI:0915”(physical association)	0.000
comEA	FAM153A	psi-mi:“MI:0915”(physical association)	0.000

BioGRID (12): FAM153A (Affinity Capture-MS), FAM153A (Two-hybrid), FAM153A (Affinity Capture-MS), FAM153A (Two-hybrid), FAM153A (Two-hybrid), FAM153A (Affinity Capture-MS), ANKRD13A (Affinity Capture-MS), EDC3 (Affinity Capture-MS), ANKRD13D (Affinity Capture-MS), DHX32 (Affinity Capture-MS), KIF3A (Affinity Capture-MS), FAM153A (Affinity Capture-MS)

ESM2 similar proteins: A0A0J9YWL9, A0A0J9YY54, A5D7L8, A6NEF3, A6NI86, B2KFW1, B4DH59, D3YZV8, E9Q6E9, F1LWT0, F6QRE9, H0YKK7, O15069, P17040, P17564, P21263, P51843, P62521, P79386, Q0P6D6, Q13342, Q2EG98, Q2KI51, Q3BBV2, Q4VC44, Q5F378, Q5QGU6, Q63560, Q6ITT4, Q6P5H2, Q6ZQX7, Q86T75, Q8CHD8, Q8IWY8, Q8N660, Q8N693, Q99PG2, Q9BE18, Q9BG93, Q9BG94

Diamond homologs: P0C7A2, Q9UHL3

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	1
Likely pathogenic	0
Uncertain significance	34
Likely benign	0
Benign	0

Top pathogenic / likely-pathogenic (1)

Variant ID	HGVS	Classification
625704	GRCh37/hg19 5q35.2-35.3(chr5:176305543-177422876)	Pathogenic

SpliceAI

3544 predictions. Top by Δscore:

Variant	Effect	Δscore
5:177724293:A:AC	donor_gain	1.0000
5:177724294:C:CC	donor_gain	1.0000
5:177724294:CA:C	donor_gain	1.0000
5:177724294:CACTT:C	donor_gain	1.0000
5:177724298:T:TA	donor_gain	1.0000
5:177724867:G:C	acceptor_gain	1.0000
5:177724867:G:GC	acceptor_gain	1.0000
5:177724871:CCA:C	acceptor_gain	1.0000
5:177724872:C:T	acceptor_gain	1.0000
5:177724872:CA:C	acceptor_gain	1.0000
5:177724873:A:AC	acceptor_gain	1.0000
5:177724873:A:C	acceptor_gain	1.0000
5:177724873:A:T	acceptor_gain	1.0000
5:177739598:A:AC	donor_gain	1.0000
5:177739599:C:CC	donor_gain	1.0000
5:177740797:CTTTT:C	acceptor_gain	1.0000
5:177741250:CTTTA:C	donor_loss	1.0000
5:177741252:TTA:T	donor_loss	1.0000
5:177741253:TACCT:T	donor_loss	1.0000
5:177741255:C:CA	donor_loss	1.0000
5:177741329:CGCT:C	acceptor_gain	1.0000
5:177741331:CT:C	acceptor_gain	1.0000
5:177741333:C:CC	acceptor_gain	1.0000
5:177744968:C:CC	acceptor_gain	1.0000
5:177748634:AACTT:A	donor_loss	1.0000
5:177748635:ACTT:A	donor_loss	1.0000
5:177748636:CTT:C	donor_loss	1.0000
5:177748637:TTA:T	donor_loss	1.0000
5:177748638:TA:T	donor_loss	1.0000
5:177748639:A:AC	donor_gain	1.0000

AlphaMissense

0 scored. Top likely-pathogenic:

dbSNP variants (sampled 300 via entrez): RS1000018441 (5:177708574 T>C), RS1000106120 (5:177739350 T>C), RS1000169391 (5:177700933 C>T), RS1000338075 (5:177762576 C>T), RS1000456208 (5:177753432 A>G), RS1000557828 (5:177753766 C>T), RS1000657061 (5:177737919 A>G), RS1000754376 (5:177722464 A>G,T), RS1000802165 (5:177763544 C>A), RS1001075693 (5:177707475 G>C), RS1001338175 (5:177759770 C>T), RS1001392081 (5:177759981 CAAA>C,CAA,CAAAA), RS1001511257 (5:177749955 G>A), RS1001527010 (5:177707720 C>CAGCT), RS1001572840 (5:177699021 G>A)

Disease associations

OMIM: gene `` | disease phenotypes:

GenCC curated gene-disease

Mondo (1): Ehlers-Danlos syndrome, spondylodysplastic type (MONDO:0007526)

Orphanet (1): B4GALT7-related spondylodysplastic Ehlers-Danlos syndrome (Orphanet:75496)

HPO phenotypes

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

GWAS associations

2 associations (top):

Study	Trait	p-value
GCST005957_13	Waist-to-hip ratio adjusted for BMI (age <50)	3.000000e-07
GCST005962_42	Waist-to-hip ratio adjusted for BMI x sex x age interaction (4df test)	1.000000e-08

EFO canonical traits (3, from GWAS)

EFO ID	Trait name
EFO:0007788	BMI-adjusted waist-hip ratio
EFO:0008007	age at assessment
EFO:0008343	sex interaction measurement

MeSH disease descriptors (1)

Descriptor	Name	Tree numbers
C536201	Ehlers-Danlos syndrome, progeroid form (supp.)

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

24 total (human), top 24 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
Tobacco Smoke Pollution	decreases expression, decreases methylation	2
Aflatoxin B1	increases methylation	2
bisphenol F	decreases expression	1
sodium arsenite	increases expression	1
maleic acid	increases expression	1
2-amino-3,8-dimethylimidazo(4,5-f)quinoxaline	decreases expression	1
4-nonylphenol	affects cotreatment, increases expression	1
4-tert-octylphenol	affects cotreatment, increases expression	1
licochalcone B	increases expression	1
bisphenol S	decreases expression	1
theaflavin-3,3’-digallate	affects expression	1
Resveratrol	affects cotreatment, decreases expression	1
Amiodarone	increases expression	1
Atrazine	increases expression	1
Benzo(a)pyrene	increases methylation	1
Cocaine	increases expression	1
Copper	affects cotreatment, decreases expression	1
Heroin	increases expression	1
Progesterone	decreases expression	1
Silicon Dioxide	decreases expression	1
Thiram	increases expression	1
Urethane	increases expression	1
Valproic Acid	increases methylation	1
Okadaic Acid	decreases expression	1

Clinical trials (associated diseases)

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