FAM76A

Summary

FAM76A (family with sequence similarity 76 member A, HGNC:28530) is a protein-coding gene on chromosome 1p35.3, encoding Protein FAM76A (Q8TAV0).

Located in nucleoplasm.

Source: NCBI Gene 199870 — RefSeq curated summary.

At a glance

• Clinical variants (ClinVar): 31 total — 1 pathogenic
• MANE Select transcript: NM_152660

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:28530
Approved symbol	FAM76A
Name	family with sequence similarity 76 member A
Location	1p35.3
Locus type	gene with protein product
Status	Approved
Aliases	MGC34648
Ensembl gene	ENSG00000009780
Ensembl biotype	protein_coding
Entrez	199870

Gene structure

Transcript identifiers

Ensembl transcripts: 11 — 11 protein_coding

ENST00000010299, ENST00000234549, ENST00000373949, ENST00000373954, ENST00000419687, ENST00000446647, ENST00000530324, ENST00000894823, ENST00000894824, ENST00000912089, ENST00000944839

RefSeq mRNA: 5 — MANE Select: NM_152660 NM_001143912, NM_001143913, NM_001143914, NM_001143915, NM_152660

CCDS: CCDS309, CCDS44092, CCDS44093, CCDS44094, CCDS44095

Canonical transcript exons

ENST00000373954 — 9 exons

Exon	Start	End
ENSE00000327880	27732603	27732657
ENSE00000761751	27759526	27759627
ENSE00000761753	27749068	27749154
ENSE00000761780	27744654	27744811
ENSE00000866714	27755195	27755330
ENSE00000866716	27734031	27734183
ENSE00001206834	27725961	27726161
ENSE00001287810	27760495	27763116
ENSE00001625313	27727472	27727536

Expression profiles

Bgee: expression breadth ubiquitous, 252 present calls, max score 91.60.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 15.1470 / max 112.5685, expressed in 1800 samples.

FANTOM5 promoters (3 alternative TSS)

Promoter ID	TPM avg	Samples expressed
1741	10.9193	1787
1742	4.2233	1622
1740	0.0045	2

Top tissues by expression

272 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	91.60	gold quality
calcaneal tendon	UBERON:0003701	88.73	gold quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	85.40	gold quality
sural nerve	UBERON:0015488	85.25	gold quality
right testis	UBERON:0004534	84.74	gold quality
left testis	UBERON:0004533	84.72	gold quality
testis	UBERON:0000473	84.43	gold quality
secondary oocyte	CL:0000655	83.77	gold quality
right lobe of thyroid gland	UBERON:0001119	83.45	gold quality
right uterine tube	UBERON:0001302	82.55	gold quality
smooth muscle tissue	UBERON:0001135	82.52	gold quality
monocyte	CL:0000576	82.49	gold quality
subcutaneous adipose tissue	UBERON:0002190	82.46	gold quality
leukocyte	CL:0000738	82.38	gold quality
left lobe of thyroid gland	UBERON:0001120	82.31	gold quality
upper arm skin	UBERON:0004263	82.14	silver quality
islet of Langerhans	UBERON:0000006	82.00	gold quality
oocyte	CL:0000023	81.99	gold quality
rectum	UBERON:0001052	81.97	gold quality
thyroid gland	UBERON:0002046	81.97	gold quality
hindlimb stylopod muscle	UBERON:0004252	81.92	gold quality
mucosa of stomach	UBERON:0001199	81.87	gold quality
tibial artery	UBERON:0007610	81.58	gold quality
ectocervix	UBERON:0012249	81.58	gold quality
popliteal artery	UBERON:0002250	81.56	gold quality
tendon	UBERON:0000043	81.48	gold quality
body of uterus	UBERON:0009853	81.48	gold quality
skin of abdomen	UBERON:0001416	81.34	gold quality
granulocyte	CL:0000094	81.27	gold quality
skin of leg	UBERON:0001511	81.23	gold quality

Single-cell (SCXA)

Detected in 2 experiment(s), a significant marker in 1.

Experiment	Marker?	Max mean expression
E-ANND-3	yes	7.05
E-GEOD-83139	no	2.74

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

101 targeting FAM76A, 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-3613-3P	100.00	76.36	7965
HSA-MIR-3163	100.00	77.23	8605
HSA-MIR-6758-5P	100.00	66.21	1470
HSA-MIR-34A-5P	99.99	71.21	1784
HSA-MIR-449A	99.99	71.05	1776
HSA-MIR-539-3P	99.98	70.74	1616
HSA-MIR-485-3P	99.98	70.68	1585
HSA-MIR-520D-5P	99.98	73.34	4883
HSA-MIR-524-5P	99.98	73.43	4882
HSA-MIR-499A-5P	99.98	70.79	1323
HSA-MIR-34C-5P	99.97	70.45	1577
HSA-MIR-449B-5P	99.97	70.26	1580
HSA-MIR-3688-3P	99.97	72.02	2834
HSA-MIR-607	99.97	73.62	5593
HSA-MIR-3658	99.96	73.87	4379
HSA-MIR-6778-3P	99.96	67.29	2693
HSA-MIR-6755-5P	99.95	65.59	464
HSA-MIR-1236-3P	99.94	68.04	1695
HSA-MIR-1305	99.91	71.43	3443
HSA-MIR-10527-5P	99.91	72.28	3754
HSA-MIR-5680	99.91	69.83	3421
HSA-MIR-3671	99.90	73.04	3897
HSA-MIR-7162-3P	99.89	68.16	1682
HSA-MIR-548E-5P	99.89	72.73	4486
HSA-MIR-1343-3P	99.89	66.78	1815
HSA-MIR-6124	99.87	69.78	3551
HSA-MIR-548D-3P	99.87	70.67	4362
HSA-MIR-5582-3P	99.86	72.48	4221
HSA-MIR-548BB-3P	99.86	70.58	4354
HSA-MIR-629-3P	99.85	67.99	1875

Cross-species orthologs

4 orthologs

Organism	Symbol	Gene ID
mus_musculus	Fam76a	ENSMUSG00000028878
rattus_norvegicus	Fam76a	ENSRNOG00000011254
drosophila_melanogaster	CG4452	FBGN0035981
caenorhabditis_elegans	K04F10.7	WBGENE00019399

Paralogs (2): FAM76B (ENSG00000077458), SENP8 (ENSG00000166192)

Protein

Protein identifiers

Protein FAM76A — Q8TAV0 (reviewed: Q8TAV0)

All UniProt accessions (3): Q8TAV0, B1AJQ5, E9PQL1

UniProt curated annotations — full annotation on UniProt →

Similarity. Belongs to the FAM76 family.

Isoforms (5)

UniProt ID	Names	Canonical?
Q8TAV0-1	1	yes
Q8TAV0-2	2
Q8TAV0-3	3
Q8TAV0-4	4
Q8TAV0-5	5

RefSeq proteins (5): NP_001137384, NP_001137385, NP_001137386, NP_001137387, NP_689873* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR032017	FAM76	Family

Pfam: PF16046

UniProt features (8 total): splice variant 3, region of interest 2, chain 1, coiled-coil region 1, compositionally biased region 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q8TAV0-F1	79.24	0.54

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 145 (showing top): PAX4_01, AP2_Q3, PUJANA_CHEK2_PCC_NETWORK, GTGCCTT_MIR506, CYTAGCAAY_UNKNOWN, GATA1_04, SCHLOSSER_SERUM_RESPONSE_DN, LASTOWSKA_NEUROBLASTOMA_COPY_NUMBER_DN, CCAGGTT_MIR490, CUI_TCF21_TARGETS_2_DN, CREBP1_01, CTTTGTA_MIR524, AP2_Q6_01, AP2GAMMA_01, RODRIGUES_THYROID_CARCINOMA_POORLY_DIFFERENTIATED_DN

GO Biological Process (0):

GO Molecular Function (0):

GO Cellular Component (2): nucleoplasm (GO:0005654), nuclear speck (GO:0016607)

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
nuclear lumen	1
cellular anatomical structure	1
nuclear ribonucleoprotein granule	1

Protein interactions and networks

STRING

200 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
FAM76A	CCDC12	Q8WUD4	685
FAM76A	NPIPA7	E9PJI5	654
FAM76A	DYRK1B	Q9Y463	489
FAM76A	CIMAP1D	Q3SX64	475
FAM76A	MPDU1	O75352	446
FAM76A	NRBP1	Q9UHY1	442
FAM76A	ETFRF1	Q6IPR1	419
FAM76A	RBM42	Q9BTD8	419
FAM76A	PPP1R8	Q12972	405
FAM76A	TMEM138	Q9NPI0	395
FAM76A	TC2N	Q8N9U0	374
FAM76A	PLEKHB2	Q96CS7	367
FAM76A	DYRK1A	Q13627	355
FAM76A	FKBP7	Q9Y680	352
FAM76A	PRPF18	Q99633	348

IntAct

4 interactions, top by confidence:

A	B	Type	Score
SPTLC1	SPTLC2	psi-mi:“MI:0914”(association)	0.680
FAM76A	SMC3	psi-mi:“MI:0915”(physical association)	0.400
KMT5C	CBX4	psi-mi:“MI:0914”(association)	0.350

BioGRID (38): SMC3 (Proximity Label-MS), FAM76A (Affinity Capture-MS), NSRP1 (Affinity Capture-MS), FAM76B (Affinity Capture-MS), G3BP2 (Affinity Capture-MS), TOX4 (Affinity Capture-MS), PPP1R10 (Affinity Capture-MS), YY1 (Affinity Capture-MS), CCNL1 (Affinity Capture-MS), FAM76A (Affinity Capture-MS), PRPF40A (Affinity Capture-MS), PRPF4B (Affinity Capture-MS), FAM76A (Affinity Capture-MS), FAM76A (Affinity Capture-MS), MFAP1 (Affinity Capture-MS)

ESM2 similar proteins: A4FVD8, A5D7H2, O14795, O43237, O55047, O70585, O75446, O88574, P58405, P84060, Q02241, Q0VA03, Q13033, Q14161, Q28H91, Q2TAD4, Q4KUS2, Q4R5P6, Q5EA89, Q5HYJ3, Q5R7U7, Q5RE09, Q5SQF8, Q5ZJ65, Q62768, Q6NYV5, Q6PBM7, Q6PDL0, Q80XP8, Q80YA9, Q811S7, Q86UE8, Q8BIK4, Q8C0V0, Q8CBY8, Q8TAV0, Q8WXI2, Q90ZY6, Q922G2, Q96EZ8

Diamond homologs: Q566M1, Q5EA89, Q5HYJ3, Q5ZJ65, Q6DEE7, Q6PBM7, Q80XP8, Q8TAV0, Q922G2

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	1
Likely pathogenic	0
Uncertain significance	21
Likely benign	0
Benign	0

Top pathogenic / likely-pathogenic (1)

Variant ID	HGVS	Classification
4279402	GRCh37/hg19 1p36.11-35.3(chr1:27408121-28103364)x1	Pathogenic

SpliceAI

1451 predictions. Top by Δscore:

Variant	Effect	Δscore
1:27726158:CAAGG:C	donor_loss	1.0000
1:27726160:AGG:A	donor_loss	1.0000
1:27726161:GGTG:G	donor_loss	1.0000
1:27726162:G:GA	donor_loss	1.0000
1:27727516:GAC:G	donor_gain	1.0000
1:27727533:A:T	donor_gain	1.0000
1:27732601:A:AG	acceptor_gain	1.0000
1:27732602:G:GA	acceptor_gain	1.0000
1:27732602:GT:G	acceptor_gain	1.0000
1:27732602:GTA:G	acceptor_gain	1.0000
1:27732602:GTAAA:G	acceptor_gain	1.0000
1:27734028:A:AG	acceptor_gain	1.0000
1:27734029:A:AT	acceptor_loss	1.0000
1:27734029:A:G	acceptor_gain	1.0000
1:27734030:G:GG	acceptor_gain	1.0000
1:27734030:G:GT	acceptor_loss	1.0000
1:27734030:GCC:G	acceptor_gain	1.0000
1:27734030:GCCC:G	acceptor_gain	1.0000
1:27734030:GCCCA:G	acceptor_gain	1.0000
1:27734166:A:T	donor_gain	1.0000
1:27734180:GAAG:G	donor_gain	1.0000
1:27734184:G:GA	donor_loss	1.0000
1:27734185:T:A	donor_loss	1.0000
1:27744652:A:AC	acceptor_loss	1.0000
1:27744653:G:GT	acceptor_loss	1.0000
1:27744653:GGT:G	acceptor_gain	1.0000
1:27744653:GGTA:G	acceptor_gain	1.0000
1:27750203:G:GT	donor_gain	1.0000
1:27755327:GAAG:G	donor_gain	1.0000
1:27755328:AAG:A	donor_loss	1.0000

AlphaMissense

2030 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
1:27726099:T:C	C7R	1.000
1:27726100:G:A	C7Y	1.000
1:27726101:C:G	C7W	1.000
1:27726108:T:C	C10R	1.000
1:27726136:T:C	L19P	1.000
1:27726154:T:C	L25P	1.000
1:27726156:T:A	C26S	1.000
1:27726156:T:C	C26R	1.000
1:27726157:G:A	C26Y	1.000
1:27726157:G:C	C26S	1.000
1:27726158:C:G	C26W	1.000
1:27727475:T:A	C29S	1.000
1:27727475:T:C	C29R	1.000
1:27727476:G:C	C29S	1.000
1:27727502:T:A	C38S	1.000
1:27727502:T:C	C38R	1.000
1:27727503:G:A	C38Y	1.000
1:27727503:G:C	C38S	1.000
1:27727503:G:T	C38F	1.000
1:27727504:C:G	C38W	1.000
1:27727511:T:A	C41S	1.000
1:27727511:T:C	C41R	1.000
1:27727512:G:A	C41Y	1.000
1:27727512:G:C	C41S	1.000
1:27727512:G:T	C41F	1.000
1:27727513:C:G	C41W	1.000
1:27727515:G:C	R42T	1.000
1:27727515:G:T	R42M	1.000
1:27727516:G:C	R42S	1.000
1:27727516:G:T	R42S	1.000

dbSNP variants (sampled 300 via entrez): RS1000133444 (1:27752143 A>G), RS1000174589 (1:27724396 T>A,G), RS1000213501 (1:27749394 G>C,T), RS1000265108 (1:27743361 C>T), RS1000337701 (1:27743654 A>G), RS1000455933 (1:27736878 C>T), RS1000559580 (1:27726707 G>A,T), RS1000564132 (1:27749568 G>T), RS1000588737 (1:27751587 C>T), RS1000673039 (1:27742103 A>T), RS1000830864 (1:27739716 A>G), RS1000847628 (1:27737168 C>G,T), RS1000927266 (1:27762485 G>A), RS1000959494 (1:27748126 T>G), RS1000980361 (1:27746389 A>G)

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

0 associations (top):

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

23 total (human), top 23 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
sodium arsenite	affects methylation, decreases expression	2
Benzo(a)pyrene	affects methylation	2
triphenyl phosphate	affects expression	1
butyraldehyde	decreases expression	1
potassium chromate(VI)	affects cotreatment, decreases expression	1
epigallocatechin gallate	decreases expression, affects cotreatment	1
abrine	decreases expression	1
bisphenol S	affects cotreatment, increases expression	1
Bortezomib	increases expression	1
Resveratrol	affects cotreatment, increases expression	1
Sunitinib	increases expression	1
Acetaminophen	increases expression	1
Caffeine	increases phosphorylation	1
Dexamethasone	affects cotreatment, increases expression	1
Doxorubicin	decreases expression	1
Indomethacin	affects cotreatment, increases expression	1
Methyl Methanesulfonate	increases expression	1
Plant Extracts	affects cotreatment, increases expression	1
Smoke	decreases expression	1
Tobacco Smoke Pollution	decreases expression	1
1-Methyl-3-isobutylxanthine	affects cotreatment, increases expression	1
Aflatoxin B1	increases methylation	1
Antirheumatic Agents	increases expression	1

Clinical trials (associated diseases)

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