FAM110D

Summary

FAM110D (family with sequence similarity 110 member D, HGNC:25860) is a protein-coding gene on chromosome 1p36.11, encoding Protein FAM110D (Q8TAY7).

At a glance

• GWAS associations: 3
• Clinical variants (ClinVar): 40 total
• MANE Select transcript: NM_024869

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:25860
Approved symbol	FAM110D
Name	family with sequence similarity 110 member D
Location	1p36.11
Locus type	gene with protein product
Status	Approved
Aliases	FLJ14050
Ensembl gene	ENSG00000197245
Ensembl biotype	protein_coding
OMIM	621327
Entrez	79927

Gene structure

Transcript identifiers

Ensembl transcripts: 6 — 6 protein_coding

ENST00000374268, ENST00000880266, ENST00000880267, ENST00000880268, ENST00000956779, ENST00000956780

RefSeq mRNA: 1 — MANE Select: NM_024869 NM_024869

CCDS: CCDS41285

Canonical transcript exons

ENST00000374268 — 2 exons

Exon	Start	End
ENSE00001420161	26159079	26159126
ENSE00001462968	26161212	26163962

Expression profiles

Bgee: expression breadth ubiquitous, 162 present calls, max score 79.82.

FANTOM5 (CAGE): breadth broad, TPM avg 0.8262 / max 19.7179, expressed in 337 samples.

FANTOM5 promoters (2 alternative TSS)

Promoter ID	TPM avg	Samples expressed
1559	0.4143	241
1560	0.4119	210

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
left uterine tube	UBERON:0001303	79.82	gold quality
apex of heart	UBERON:0002098	77.00	gold quality
mucosa of stomach	UBERON:0001199	76.97	gold quality
omental fat pad	UBERON:0010414	76.62	gold quality
peritoneum	UBERON:0002358	76.58	gold quality
inferior olivary complex	UBERON:0002127	75.73	gold quality
adipose tissue of abdominal region	UBERON:0007808	75.68	gold quality
subcutaneous adipose tissue	UBERON:0002190	75.12	gold quality
body of uterus	UBERON:0009853	73.34	gold quality
dorsal motor nucleus of vagus nerve	UBERON:0002870	73.05	gold quality
right lobe of thyroid gland	UBERON:0001119	72.93	gold quality
lower esophagus muscularis layer	UBERON:0035833	72.92	gold quality
lower esophagus	UBERON:0013473	72.80	gold quality
adipose tissue	UBERON:0001013	72.40	gold quality
cardiac ventricle	UBERON:0002082	72.27	gold quality
heart left ventricle	UBERON:0002084	72.23	gold quality
esophagogastric junction muscularis propria	UBERON:0035841	72.21	gold quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	72.13	silver quality
gluteal muscle	UBERON:0002000	72.06	gold quality
connective tissue	UBERON:0002384	71.78	gold quality
endocervix	UBERON:0000458	71.21	gold quality
hindlimb stylopod muscle	UBERON:0004252	71.21	gold quality
left coronary artery	UBERON:0001626	71.19	gold quality
tibial nerve	UBERON:0001323	71.13	gold quality
right coronary artery	UBERON:0001625	70.62	gold quality
ectocervix	UBERON:0012249	70.57	gold quality
coronary artery	UBERON:0001621	70.43	gold quality
upper lobe of left lung	UBERON:0008952	70.26	gold quality
heart	UBERON:0000948	69.51	gold quality
left lobe of thyroid gland	UBERON:0001120	69.41	gold quality

Single-cell (SCXA)

Detected in 5 experiment(s), a significant marker in 4.

Experiment	Marker?	Max mean expression
E-GEOD-111727	yes	3781.30
E-GEOD-75140	yes	148.67
E-MTAB-10287	yes	62.38
E-ANND-3	yes	5.47
E-CURD-112	no	2.55

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

11 targeting FAM110D, 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-3663-3P	99.84	70.39	798
HSA-MIR-3202	99.66	67.70	2737
HSA-MIR-12123	99.52	71.79	2990
HSA-MIR-4667-3P	99.26	65.45	1608
HSA-MIR-4291	99.20	68.88	2969
HSA-MIR-892C-5P	99.16	70.56	2116
HSA-MIR-3619-5P	99.00	68.87	2308
HSA-MIR-214-3P	98.71	68.12	2128
HSA-MIR-761	98.71	68.07	2051
HSA-MIR-506-5P	98.02	67.41	1065
HSA-MIR-4783-5P	79.94	61.48	12

Literature-anchored findings (GeneRIF, showing 1)

• Three Novel Genetic Variants in the FAM110D, CACNA1A, and NLRP12 Genes Are Associated With Susceptibility to Hypertension Among Dai People. (PMID:33621312)

Cross-species orthologs

3 orthologs

Organism	Symbol	Gene ID
danio_rerio	fam110d	ENSDARG00000062517
mus_musculus	Fam110d	ENSMUSG00000050105
rattus_norvegicus	Fam110d	ENSRNOG00000016491

Paralogs (3): FAM110A (ENSG00000125898), FAM110B (ENSG00000169122), FAM110C (ENSG00000184731)

Protein

Protein identifiers

Protein FAM110D — Q8TAY7 (reviewed: Q8TAY7)

All UniProt accessions (1): Q8TAY7

UniProt curated annotations — full annotation on UniProt →

Similarity. Belongs to the FAM110 family.

RefSeq proteins (1): NP_079145* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR025739	FAM110_N	Domain
IPR025740	FAM110	Family
IPR025741	FAM110_C	Domain

Pfam: PF14160, PF14161

UniProt features (8 total): region of interest 3, compositionally biased region 3, chain 1, sequence variant 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q8TAY7-F1	62.35	0.06

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 57 (showing top): HUMMERICH_MALIGNANT_SKIN_TUMOR_UP, GGGTGGRR_PAX4_03, IRF7_01, ZIC1_01, TATA_C, AACTTT_UNKNOWN, TGGAAA_NFAT_Q4_01, chr1p36, TGATTTRY_GFI1_01, ALK_DN.V1_UP, MIR4291, MIR3619_5P, MIR214_3P, MIR761, AMEF2_Q6

GO Biological Process (0):

GO Molecular Function (0):

GO Cellular Component (0):

Protein interactions and networks

STRING

366 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
FAM110D	SMTNL2	Q2TAL5	469
FAM110D	KAZN	Q674X7	444
FAM110D	NYAP2	Q9P242	425
FAM110D	PDIK1L	Q8N165	423
FAM110D	N4BP3	O15049	406
FAM110D	EVX1	P49640	385
FAM110D	AK5	Q9Y6K8	378
FAM110D	TMEM35A	Q53FP2	370
FAM110D	ADAP2	Q9NPF8	360
FAM110D	MESP1	Q9BRJ9	344
FAM110D	TIAM2	Q8IVF5	309
FAM110D	SLC34A1	Q06495	301
FAM110D	NRARP	Q7Z6K4	297
FAM110D	RTP4	Q96DX8	282
FAM110D	IGSF1	Q8N6C5	269
FAM110D	CROCC2	H7BZ55	269

IntAct

120 interactions, top by confidence:

A	B	Type	Score
PNMA2	CCDC85C	psi-mi:“MI:0914”(association)	0.530
FAM110D	DLG4	psi-mi:“MI:0407”(direct interaction)	0.440
FAM110D	DLG1	psi-mi:“MI:0407”(direct interaction)	0.440
FAM110D	SYNJ2BP	psi-mi:“MI:0407”(direct interaction)	0.440
FAM110D	DLG2	psi-mi:“MI:0407”(direct interaction)	0.440
FAM110D	SNTA1	psi-mi:“MI:0407”(direct interaction)	0.440
FAM110D	TAX1BP3	psi-mi:“MI:0407”(direct interaction)	0.440
FAM110D	SNTG1	psi-mi:“MI:0407”(direct interaction)	0.440
FAM110D	DLG3	psi-mi:“MI:0407”(direct interaction)	0.440
FAM110D	SNTB1	psi-mi:“MI:0407”(direct interaction)	0.440
FAM110D	PDZRN3	psi-mi:“MI:0407”(direct interaction)	0.440
MAGI3	FAM110D	psi-mi:“MI:0407”(direct interaction)	0.440
FAM110D	IL16	psi-mi:“MI:0407”(direct interaction)	0.440
FAM110D	PTPN3	psi-mi:“MI:0407”(direct interaction)	0.440
FAM110D	SCRIB	psi-mi:“MI:0407”(direct interaction)	0.440
MAST2	FAM110D	psi-mi:“MI:0407”(direct interaction)	0.440
FAM110D	PDZD2	psi-mi:“MI:0407”(direct interaction)	0.440
FAM110D	SNX27	psi-mi:“MI:0407”(direct interaction)	0.440
FAM110D	MAGI2	psi-mi:“MI:0407”(direct interaction)	0.440
FAM110D	MAST1	psi-mi:“MI:0407”(direct interaction)	0.440
FAM110D	PDZD7	psi-mi:“MI:0407”(direct interaction)	0.440
FAM110D	PDZRN4	psi-mi:“MI:0407”(direct interaction)	0.440
SNTG2	FAM110D	psi-mi:“MI:0407”(direct interaction)	0.440

BioGRID (26): NDUFA2 (Affinity Capture-MS), ACBD6 (Affinity Capture-MS), MAPK8 (Affinity Capture-MS), ZNF703 (Affinity Capture-MS), TRIP6 (Affinity Capture-MS), PNMA2 (Affinity Capture-MS), RCOR3 (Affinity Capture-MS), ZNF618 (Affinity Capture-MS), GAPVD1 (Affinity Capture-MS), FAM83H (Affinity Capture-MS), HOXB8 (Affinity Capture-MS), MAPK9 (Affinity Capture-MS), RCOR1 (Affinity Capture-MS), KDM1A (Affinity Capture-MS), USP4 (Affinity Capture-MS)

ESM2 similar proteins: A2A9T0, A2AEV7, A2AHG0, A5PKL7, A6H7I7, A6NCL7, A6NKL6, B8ZZ34, D3ZZN9, J3QNX5, O60299, Q0PHV7, Q1W6H9, Q2KJ38, Q2M3G4, Q2M3V2, Q3LUD4, Q3SX20, Q4KLY2, Q4KMQ1, Q4QRD7, Q53LP3, Q58DG5, Q5RKJ0, Q5SW24, Q6DG50, Q6NUJ5, Q6NY19, Q6PJ61, Q6ZW31, Q7TN08, Q7TNF9, Q80X91, Q8BLS7, Q8CHM3, Q8IX07, Q8IXH6, Q8K1Q4, Q8R184, Q8TAY7

Diamond homologs: A6H7I7, Q1W6H9, Q58DG5, Q80X91, Q8R184, Q8TAY7, Q8VE94, Q9BQ89, Q2KJ38, Q4QRD7, Q5BJX5, Q5R5R3, Q5RKJ0, Q8C739, Q8TC76

SIGNOR signaling

0 interactions.

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 79 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
Ras activation upon Ca2+ influx through NMDA receptor	5	57.1×	1e-06
Unblocking of NMDA receptors, glutamate binding and activation	5	54.4×	1e-06
Negative regulation of NMDA receptor-mediated neuronal transmission	5	54.4×	1e-06
Long-term potentiation	5	47.6×	2e-06
Assembly and cell surface presentation of NMDA receptors	9	45.7×	2e-11
Neurexins and neuroligins	10	39.4×	9e-12
Protein-protein interactions at synapses	6	31.9×	1e-06
Neuronal System	6	5.3×	9e-03

GO biological processes:

GO term	Partners	Fold	FDR
establishment or maintenance of epithelial cell apical/basal polarity	11	84.1×	1e-16
protein localization to synapse	6	60.5×	6e-08
receptor clustering	7	57.5×	6e-09
regulation of postsynaptic membrane neurotransmitter receptor levels	7	45.6×	2e-08
establishment of cell polarity	5	25.2×	7e-05
protein-containing complex assembly	9	13.5×	1e-06
cell-cell adhesion	10	13.4×	3e-07
chemical synaptic transmission	7	7.1×	1e-03

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	39
Likely benign	1
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

261 predictions. Top by Δscore:

Variant	Effect	Δscore
1:26159124:GAG:G	donor_gain	0.9900
1:26159127:GTG:G	donor_loss	0.9900
1:26159128:T:A	donor_loss	0.9900
1:26159765:G:GT	donor_gain	0.9900
1:26161207:TGCA:T	acceptor_loss	0.9900
1:26161208:GCA:G	acceptor_loss	0.9900
1:26161209:CA:C	acceptor_loss	0.9900
1:26161210:A:AG	acceptor_gain	0.9900
1:26161210:A:AT	acceptor_loss	0.9900
1:26161211:G:GG	acceptor_gain	0.9900
1:26161211:GGTCA:G	acceptor_gain	0.9900
1:26159127:G:GG	donor_gain	0.9800
1:26159127:G:GA	donor_gain	0.9700
1:26159128:T:TC	donor_gain	0.9700
1:26161211:GGTC:G	acceptor_gain	0.9700
1:26159126:GGT:G	donor_gain	0.9600
1:26159129:G:GG	donor_gain	0.9600
1:26159129:GAGTG:G	donor_loss	0.9600
1:26159130:A:AC	donor_gain	0.9600
1:26159765:G:T	acceptor_gain	0.9600
1:26161211:GGT:G	acceptor_gain	0.9600
1:26159125:AGGTG:A	donor_gain	0.9500
1:26159124:GAGGT:G	donor_gain	0.9400
1:26161207:T:TA	acceptor_gain	0.9300
1:26161210:AG:A	acceptor_gain	0.9200
1:26161211:GG:G	acceptor_gain	0.9200
1:26161319:TCCAG:T	acceptor_gain	0.9100
1:26159123:AGAGG:A	donor_gain	0.8900
1:26159125:AG:A	donor_gain	0.8800
1:26159126:GG:G	donor_gain	0.8800

AlphaMissense

1697 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
1:26161366:A:C	K25N	0.999
1:26161366:A:T	K25N	0.999
1:26161374:A:G	Y28C	0.999
1:26161784:T:C	F165L	0.999
1:26161785:T:C	F165S	0.999
1:26161786:C:A	F165L	0.999
1:26161786:C:G	F165L	0.999
1:26162049:T:A	I253N	0.999
1:26162049:T:C	I253T	0.999
1:26162056:G:C	W255C	0.999
1:26162056:G:T	W255C	0.999
1:26161353:T:C	L21P	0.998
1:26161373:T:C	Y28H	0.998
1:26161787:T:C	F166L	0.998
1:26161788:T:C	F166S	0.998
1:26161789:C:A	F166L	0.998
1:26161789:C:G	F166L	0.998
1:26162049:T:G	I253S	0.998
1:26162054:T:A	W255R	0.998
1:26162054:T:C	W255R	0.998
1:26161374:A:C	Y28S	0.997
1:26161377:T:A	V29D	0.997
1:26161797:G:A	C169Y	0.997
1:26162058:T:C	L256P	0.997
1:26161365:A:T	K25I	0.996
1:26161373:T:G	Y28D	0.996
1:26161381:G:C	K30N	0.996
1:26161381:G:T	K30N	0.996
1:26161785:T:G	F165C	0.996
1:26161787:T:A	F166I	0.996

dbSNP variants (sampled 300 via entrez): RS1000411501 (1:26161946 G>A), RS1001074106 (1:26158845 C>A,T), RS1001549306 (1:26162286 G>A,C,T), RS1001819806 (1:26160550 C>A,G,T), RS1001851921 (1:26164108 C>A), RS1001883102 (1:26164269 T>C), RS1001931988 (1:26163168 A>C), RS1002422694 (1:26159259 C>G), RS1002482247 (1:26157553 C>A), RS1002554067 (1:26160774 C>T), RS1002800207 (1:26159483 G>A), RS1003305189 (1:26158548 A>C,G,T), RS1004313930 (1:26157385 C>G,T), RS1004870457 (1:26159074 C>T), RS1004905245 (1:26161336 C>A,T)

Disease associations

OMIM: gene MIM:621327 | 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
GCST006979_869	Heel bone mineral density	7.000000e-16
GCST008163_386	Height	2.000000e-06
GCST90020028_522	Hip circumference adjusted for BMI	2.000000e-08

EFO canonical traits (2, from GWAS)

EFO ID	Trait name
EFO:0009270	heel bone mineral density
EFO:0008039	BMI-adjusted hip circumference

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

10 total (human), top 10 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
bisphenol A	affects cotreatment, decreases methylation	1
Resveratrol	decreases expression, affects cotreatment	1
Sunitinib	decreases expression	1
Fulvestrant	decreases methylation, affects cotreatment	1
Arsenic	decreases methylation	1
Benzo(a)pyrene	increases methylation	1
Copper	affects cotreatment, decreases expression	1
Tretinoin	decreases expression	1
Triclosan	decreases expression	1
Particulate Matter	increases methylation	1

Clinical trials (associated diseases)

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