FAM170A

Summary

FAM170A (family with sequence similarity 170 member A, HGNC:27963) is a protein-coding gene on chromosome 5q23.1, encoding Protein FAM170A (A1A519). Acts as a nuclear transcription factor that positively regulates the expression of heat shock genes.

Predicted to enable DNA binding activity and zinc ion binding activity. Involved in positive regulation of DNA-templated transcription and transcription by RNA polymerase II. Located in nucleus.

Source: NCBI Gene 340069 — RefSeq curated summary.

At a glance

• GWAS associations: 10
• Clinical variants (ClinVar): 84 total — 2 likely-pathogenic
• MANE Select transcript: NM_001367956

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:27963
Approved symbol	FAM170A
Name	family with sequence similarity 170 member A
Location	5q23.1
Locus type	gene with protein product
Status	Approved
Aliases	ZNFD
Ensembl gene	ENSG00000164334
Ensembl biotype	protein_coding
OMIM	618401
Entrez	340069

Gene structure

Transcript identifiers

Ensembl transcripts: 5 — 5 protein_coding

ENST00000335286, ENST00000379555, ENST00000504819, ENST00000695508, ENST00000695509

RefSeq mRNA: 3 — MANE Select: NM_001367956 NM_001163991, NM_001367956, NM_182761

CCDS: CCDS43353, CCDS54889, CCDS93765

Canonical transcript exons

ENST00000695508 — 5 exons

Exon	Start	End
ENSE00001312281	119632748	119632888
ENSE00001724310	119633960	119634734
ENSE00002056606	119629558	119629838
ENSE00003479929	119635028	119635086
ENSE00003964067	119635700	119635822

Expression profiles

Bgee: expression breadth broad, 57 present calls, max score 86.53.

FANTOM5 (CAGE): breadth tissue_specific, TPM avg 0.0583 / max 55.4835, expressed in 3 samples.

FANTOM5 promoters (1 alternative TSS)

Promoter ID	TPM avg	Samples expressed
58156	0.0583	3

Top tissues by expression

195 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	86.53	gold quality
left testis	UBERON:0004533	81.64	gold quality
right testis	UBERON:0004534	80.07	gold quality
testis	UBERON:0000473	79.61	gold quality
sperm	CL:0000019	71.03	gold quality
myocardium	UBERON:0002349	66.97	gold quality
buccal mucosa cell	CL:0002336	66.62	gold quality
cartilage tissue	UBERON:0002418	61.46	gold quality
tendon of biceps brachii	UBERON:0008188	60.64	gold quality
decidua	UBERON:0002450	60.23	gold quality
skeletal muscle tissue of rectus abdominis	UBERON:0004511	59.87	gold quality
gingiva	UBERON:0001828	58.52	gold quality
secondary oocyte	CL:0000655	58.11	gold quality
sural nerve	UBERON:0015488	56.50	silver quality
trabecular bone tissue	UBERON:0002483	56.46	gold quality
oocyte	CL:0000023	56.20	gold quality
adult organism	UBERON:0007023	56.06	silver quality
gingival epithelium	UBERON:0001949	55.36	gold quality
thymus	UBERON:0002370	55.28	gold quality
cerebellar vermis	UBERON:0004720	55.17	gold quality
medial globus pallidus	UBERON:0002477	54.91	gold quality
skeletal muscle tissue of biceps brachii	UBERON:0004502	54.88	gold quality
oral cavity	UBERON:0000167	54.57	gold quality
mammalian vulva	UBERON:0000997	54.52	gold quality
esophagus squamous epithelium	UBERON:0006920	54.01	gold quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	53.96	gold quality
jejunal mucosa	UBERON:0000399	53.11	gold quality
mammary duct	UBERON:0001765	52.27	gold quality
pons	UBERON:0000988	51.89	gold quality
globus pallidus	UBERON:0001875	51.72	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	no	1.31

Regulation

Is transcription factor: yes

Downstream targets (CollecTRI)

1 targets.

Target	Regulation
AKT1

miRNA regulators (miRDB)

16 targeting FAM170A, 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-629-3P	99.85	67.99	1875
HSA-MIR-4659A-3P	99.80	72.62	4248
HSA-MIR-4659B-3P	99.80	72.62	4248
HSA-MIR-4713-5P	99.78	67.80	1794
HSA-MIR-556-3P	99.74	68.75	1203
HSA-MIR-4666A-5P	99.41	69.72	1887
HSA-MIR-942-5P	99.41	68.40	1977
HSA-MIR-4464	98.95	67.73	820
HSA-MIR-4748	98.95	67.53	810
HSA-MIR-7113-3P	98.75	65.71	1120
HSA-MIR-6867-3P	98.12	66.07	1305
HSA-MIR-4469	97.93	65.81	1319
HSA-MIR-4287	97.55	67.24	1247
HSA-MIR-4685-3P	97.55	67.35	1255
HSA-MIR-6813-3P	95.78	63.78	540
HSA-MIR-151A-3P	95.52	65.29	516

Literature-anchored findings (GeneRIF, showing 1)

• Data indicate that ZNFD is probably a new type of C(2)H(2) zinc finger protein that may activate AP1 transcriptional activities. (PMID:20162441)

Cross-species orthologs

2 orthologs

Organism	Symbol	Gene ID
mus_musculus	Fam170a	ENSMUSG00000035420
rattus_norvegicus	Fam170a	ENSRNOG00000015834

Protein

Protein identifiers

Protein FAM170A — A1A519 (reviewed: A1A519)

Alternative names: Zinc finger domain-containing protein, Zinc finger protein ZNFD

All UniProt accessions (3): A0A8Q3SHZ7, A1A519, D6RIE9

UniProt curated annotations — full annotation on UniProt →

Function. Acts as a nuclear transcription factor that positively regulates the expression of heat shock genes. Binds to heat shock promoter elements (HSE).

Subcellular location. Nucleus.

Tissue specificity. Expressed strongly in testis and brain and weakly in prostate, spleen, pancreas and uterus.

Domain organisation. The N-terminus is necessary for nuclear localization. The C-terminus is necessary for transcriptional activity.

Similarity. Belongs to the FAM170 family.

Isoforms (4)

UniProt ID	Names	Canonical?
A1A519-1	1	yes
A1A519-2	2
A1A519-3	3
A1A519-4	4

RefSeq proteins (3): NP_001157463, NP_001354885, NP_877438 (=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR040879	Spt46-like	Family

Pfam: PF17734

UniProt features (17 total): splice variant 5, region of interest 4, compositionally biased region 3, modified residue 2, chain 1, zinc finger region 1, sequence variant 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-A1A519-F1	57.06	0.11

Functional residue map

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

Post-translational modifications (2): 315, 217

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 45 (showing top): GSE18804_SPLEEN_MACROPHAGE_VS_COLON_TUMORAL_MACROPHAGE_DN, TGACCTY_ERR1_Q2, GGGTGGRR_PAX4_03, COUP_01, HNF4_DR1_Q3, HNF4_01, TGACATY_UNKNOWN, PPAR_DR1_Q2, RYTTCCTG_ETS2_B, GOBP_FERTILIZATION, TGGAAA_NFAT_Q4_01, PPARG_01, COUP_DR1_Q6, HNF4ALPHA_Q6, GSE13887_HEALTHY_VS_LUPUS_RESTING_CD4_TCELL_UP

GO Biological Process (3): transcription by RNA polymerase II (GO:0006366), fertilization (GO:0009566), positive regulation of DNA-templated transcription (GO:0045893)

GO Molecular Function (3): DNA binding (GO:0003677), zinc ion binding (GO:0008270), metal ion binding (GO:0046872)

GO Cellular Component (1): nucleus (GO:0005634)

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
DNA-templated transcription	2
sexual reproduction	1
reproductive process	1
regulation of DNA-templated transcription	1
positive regulation of RNA biosynthetic process	1
nucleic acid binding	1
transition metal ion binding	1
cation binding	1
intracellular membrane-bounded organelle	1

Protein interactions and networks

STRING

442 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
FAM170A	ZMYND19	Q96E35	826
FAM170A	TUBA4A	P05215	762
FAM170A	MCHR1	Q99705	715
FAM170A	TUBB2A	Q13885	650
FAM170A	TUBB	P05218	648
FAM170A	DEAF1	O75398	587
FAM170A	SSMEM1	Q8WWF3	533
FAM170A	ZCCHC8	Q6NZY4	467
FAM170A	BUB3	O43684	446
FAM170A	SPEM1	Q8N4L4	433
FAM170A	FTMT	Q8N4E7	427
FAM170A	TRAF3IP3	Q9Y228	416
FAM170A	MYNN	Q9NPC7	399
FAM170A	C16orf87	Q6PH81	369
FAM170A	TNP1	P09430	350
FAM170A	SNCAIP	Q9Y6H5	350

IntAct

5 interactions, top by confidence:

A	B	Type	Score
FAM170A	NDC80	psi-mi:“MI:0914”(association)	0.350
FAM170A	RPSA2	psi-mi:“MI:0914”(association)	0.350
FAM170A	MCM3AP	psi-mi:“MI:0914”(association)	0.350
INSR	BLTP3B	psi-mi:“MI:0914”(association)	0.350

BioGRID (43): CSNK1A1 (Affinity Capture-MS), CSNK1A1L (Affinity Capture-MS), ZNF358 (Affinity Capture-MS), USP7 (Affinity Capture-MS), SPC24 (Affinity Capture-MS), VAPB (Affinity Capture-MS), VAPA (Affinity Capture-MS), MIER1 (Affinity Capture-MS), DGCR14 (Affinity Capture-MS), SPC25 (Affinity Capture-MS), QSER1 (Affinity Capture-MS), TRIM27 (Affinity Capture-MS), ZNF703 (Affinity Capture-MS), CSNK1A1L (Affinity Capture-MS), CSNK1A1 (Affinity Capture-MS)

ESM2 similar proteins: A0JNH1, A1A519, A4IH95, A6H7B4, A6NFA0, A6NGY1, A6NMN3, B2RQL2, D2J0Y4, F1N8V3, F1RDM5, P59598, Q05AH6, Q0P5X5, Q0VET5, Q14B48, Q1RN00, Q2YDE2, Q32LN6, Q3UXL4, Q4R7L6, Q52KN3, Q5EBJ4, Q5M831, Q5RJL0, Q5T0L3, Q64ET8, Q66H04, Q66LM5, Q66LM6, Q68A65, Q68D20, Q6DIA7, Q6GQV1, Q6NWJ0, Q6ZRS4, Q6ZVD7, Q80VY2, Q811R2, Q8BHW6

Diamond homologs: A1A519, A6NMN3, E9PXT9, Q2YDE2, Q4FZF2, Q4R7L6, Q5T0L3, Q66LM5, Q66LM6

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	2
Uncertain significance	73
Likely benign	8
Benign	0

Top pathogenic / likely-pathogenic (2)

Variant ID	HGVS	Classification
3024385	GRCh38/hg38 5q23.1(chr5:119555413-119745470)	Likely pathogenic
393534	GRCh37/hg19 5q23.1(chr5:118890915-119082631)x1	Likely pathogenic

SpliceAI

603 predictions. Top by Δscore:

Variant	Effect	Δscore
5:119629817:G:GT	donor_gain	1.0000
5:119629832:G:GT	donor_gain	1.0000
5:119629833:G:T	donor_gain	1.0000
5:119629835:GGAG:G	donor_gain	1.0000
5:119629836:GAGG:G	donor_gain	1.0000
5:119629839:G:GA	donor_loss	1.0000
5:119629840:T:A	donor_loss	1.0000
5:119632886:GTG:G	donor_gain	1.0000
5:119634732:G:GT	donor_gain	1.0000
5:119629818:A:T	donor_gain	0.9900
5:119629836:GAG:G	donor_gain	0.9900
5:119629839:G:GG	donor_gain	0.9900
5:119632736:T:G	acceptor_gain	0.9900
5:119632738:C:G	acceptor_gain	0.9900
5:119632747:GGA:G	acceptor_gain	0.9900
5:119632747:GGAAT:G	acceptor_gain	0.9900
5:119634731:GGAA:G	donor_gain	0.9900
5:119634735:G:GG	donor_gain	0.9900
5:119635014:T:TA	acceptor_gain	0.9900
5:119635022:A:AG	acceptor_gain	0.9900
5:119635023:C:G	acceptor_gain	0.9900
5:119629824:C:G	donor_gain	0.9800
5:119632735:A:AG	acceptor_gain	0.9800
5:119632743:CTCA:C	acceptor_loss	0.9800
5:119632744:TCA:T	acceptor_loss	0.9800
5:119632745:CAG:C	acceptor_loss	0.9800
5:119632746:A:AG	acceptor_gain	0.9800
5:119632746:A:G	acceptor_loss	0.9800
5:119632746:AG:A	acceptor_gain	0.9800
5:119632747:G:GG	acceptor_gain	0.9800

AlphaMissense

0 scored. Top likely-pathogenic:

dbSNP variants (sampled 300 via entrez): RS1000300582 (5:119635615 C>T), RS1000716691 (5:119634973 T>C), RS1001173639 (5:119630477 A>G), RS1001353768 (5:119635691 C>T), RS1001662829 (5:119631600 C>T), RS1001705722 (5:119631307 A>G), RS1001801688 (5:119635976 C>T), RS1002059940 (5:119635639 C>A), RS1002112200 (5:119635914 T>C), RS1002175969 (5:119631663 A>G), RS1003062003 (5:119627601 A>C,G), RS1004122236 (5:119633551 T>C), RS1005133942 (5:119633397 G>A), RS1005510649 (5:119629077 G>A,T), RS1006112125 (5:119634170 T>C)

Disease associations

OMIM: gene MIM:618401 | disease phenotypes: MIM:192350

GenCC curated gene-disease

Mondo (2): autism spectrum disorder (MONDO:0005258), VACTERL/vater association (MONDO:0008642)

Orphanet (2): VACTERL/VATER association (Orphanet:887), NON RARE IN EUROPE: Autism (Orphanet:106)

HPO phenotypes

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

GWAS associations

10 associations (top):

Study	Trait	p-value
GCST003772_7	Loneliness (linear analysis)	2.000000e-06
GCST004031_3	QT interval (sulfonylurea treatment interaction)	4.000000e-07
GCST004032_1	JT interval (sulfonylurea treatment interaction)	5.000000e-07
GCST005956_40	Waist-to-hip ratio adjusted for BMI	2.000000e-06
GCST005958_18	Waist-to-hip ratio adjusted for BMI (age >50)	9.000000e-07
GCST005962_27	Waist-to-hip ratio adjusted for BMI x sex x age interaction (4df test)	9.000000e-09
GCST009441_2	Age-related cognitive decline (memory) (slope of z-scores)	7.000000e-07
GCST009444_3	Age-related cognitive decline (global cognition) (slope of z-scores)	2.000000e-06
GCST009798_70	Asthma	3.000000e-11
GCST90026412_14	Severe autoimmune type 2 diabetes	9.000000e-06

EFO canonical traits (8, from GWAS)

EFO ID	Trait name
EFO:0007865	loneliness measurement
EFO:0004682	QT interval
EFO:0007922	response to sulfonylurea
EFO:0007885	JT interval
EFO:0007788	BMI-adjusted waist-hip ratio
EFO:0008007	age at assessment
EFO:0008343	sex interaction measurement
EFO:0007710	cognitive decline measurement

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

4 total (human), top 4 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
Resveratrol	affects cotreatment, decreases expression	1
Benzo(a)pyrene	decreases methylation	1
Plant Extracts	affects cotreatment, decreases expression	1
Valproic Acid	decreases methylation	1

Clinical trials (associated diseases)

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

Trial	Phase	Status	Title
NCT00391261	PHASE4	COMPLETED	An Open-label Trial of Metformin for Weight Control of Pediatric Patients on Antipsychotic Medications.
NCT01028820	PHASE4	COMPLETED	FMRI Brain Activation of Aripiprazole Treatment in Autism Spectrum Disorders
NCT01333865	PHASE4	COMPLETED	A Study of Memantine Hydrochloride (Namenda®) for Cognitive and Behavioral Impairment in Adults With Autism Spectrum Disorders
NCT01337700	PHASE4	COMPLETED	Milnacipran in Autism and the Functional Locus Coeruleus and Noradrenergic Model of Autism
NCT01695200	PHASE4	COMPLETED	Omega-3 Fatty Acids in Autism Spectrum Disorders
NCT02096952	PHASE4	COMPLETED	Methylphenidate ER Liquid Formulation in Adults With ASD and ADHD
NCT02235467	PHASE4	COMPLETED	Multisite Study: Parental Training Using Video Modelling to Develop Social Skills in Children With Autism
NCT02940574	PHASE4	COMPLETED	Neural and Behavioral Effects of Oxytocin in Autism Spectrum Disorders
NCT03333629	PHASE4	COMPLETED	Promoting Positive Outcomes for Individuals With ASD: Linking Early Detection, Treatment, and Long-term Outcomes
NCT03337646	PHASE4	COMPLETED	Evaluation of the Effect and Safety of Lisdexamfetamine in Children Aged 6-12 With ADHD and Autism
NCT03538431	PHASE4	COMPLETED	Improving Driving in Young People With Autism Spectrum Disorders
NCT03757585	PHASE4	COMPLETED	Natural Treatments for the Management of Emotional Dysregulation in Youth With Non-verbal Learning Disability (NVLD) and/or Autism Spectrum Disorders (ASD)
NCT04903353	PHASE4	COMPLETED	Pragmatic Trial Comparing Weight Gain in Children With Autism Taking Risperidone Versus Aripiprazole
NCT05063656	PHASE4	COMPLETED	Biomarker-Driven Pharmacological Treatment of Adolescents With Autism Spectrum Disorder With Gabapentin
NCT05146245	PHASE4	UNKNOWN	Safety and Pharmacokinetics of Antipsychotics in Children 2: Studying TDM in an RCT
NCT05916339	PHASE4	RECRUITING	AWARE: Management of ADHD in Autism Spectrum Disorder
NCT05954052	PHASE4	TERMINATED	A Study of Glutathione in Children With Autism Spectrum Disorder
NCT06853665	PHASE4	RECRUITING	The TEAM Study - Treatment Efficacy for Autism/Attention Using Mixed Amphetamine
NCT07054697	PHASE4	COMPLETED	Pilot-RCT With Individualized Homeopathic Treatment in the Children With Autism Spectrum Disorder
NCT07161804	PHASE4	COMPLETED	Pilot RCT Using Homeopathic Medicines in ASD
NCT07439042	PHASE4	NOT_YET_RECRUITING	Buspirone for Anxiety in Autistic Youth
NCT01302964	PHASE3	COMPLETED	Mirtazapine Treatment of Anxiety in Children and Adolescents With Pervasive Developmental Disorders
NCT01706523	PHASE3	TERMINATED	Open Label Extension Study of STX209 (Arbaclofen) in Autism Spectrum Disorders
NCT01825798	PHASE3	COMPLETED	Treatment of Overweight Induced by Antipsychotic Medication in Young People With Autism Spectrum Disorders (ASD)
NCT01972074	PHASE3	COMPLETED	Behavioral and Neural Response to Memantine in Adolescents With Autism Spectrum Disorder
NCT02985749	PHASE3	COMPLETED	A Study of Oxytocin for the Treatment of Social Impairment in Individuals With High Functioning Autism Spectrum Disorder
NCT03197922	PHASE3	COMPLETED	Treatment of Encopresis in Children With Autism Spectrum Disorders
NCT03504917	PHASE3	TERMINATED	A Study of Balovaptan in Adults With Autism Spectrum Disorder With a 2-Year Open-Label Extension
NCT03553875	PHASE3	TERMINATED	Memantine for the Treatment of Social Deficits in Youth With Disorders of Impaired Social Interactions
NCT03640156	PHASE3	COMPLETED	Modulating Socially Adaptive Mirror System Functioning in Autism by Oxytocin
NCT03715153	PHASE3	TERMINATED	Efficacy and Safety of Bumetanide Oral Liquid Formulation in Children Aged From 2 to Less Than 7 Years Old With Autism Spectrum Disorder.
NCT03715166	PHASE3	TERMINATED	Efficacy and Safety of Bumetanide Oral Liquid Formulation in Children and Adolescents Aged From 7 to Less Than 18 Years Old With Autism Spectrum Disorder
NCT04233502	PHASE3	WITHDRAWN	Efficacy and Safety of Slenyto for Insomnia in Children With ASD
NCT04578756	PHASE3	COMPLETED	Open-Label, Flexible-dose Study to Evaluate the Long-Term Safety and Tolerability of Cariprazine in the Treatment of Pediatric Participants With Schizophrenia, Bipolar I Disorder, or Autism Spectrum Disorder
NCT04623398	PHASE3	COMPLETED	Effect of Lithium in Patients With Autism Spectrum Disorder and Phelan-McDermid Syndrome (SHANK3 Haploinsufficiency)
NCT04725383	PHASE3	TERMINATED	Amitriptyline for Repetitive Behaviors in Autism Spectrum Disorders
NCT05212493	PHASE3	COMPLETED	The Effects of Medical Cannabis in Children With Autistic Spectrum Disorder
NCT05361707	PHASE3	UNKNOWN	Evaluating the Effects of Tasimelteon in Individuals With Autism Spectrum Disorder (ASD) and Sleep Disturbances
NCT05439616	PHASE3	COMPLETED	Study of Cariprazine Oral Capsules or Solution to Assess Adverse Events and Change in Irritability Due to Autism Spectrum Disorder (ASD) in Participants Aged 5-17 Years With ASD
NCT06229210	PHASE3	RECRUITING	Safety and Tolerability Trial of Lumateperone in Pediatric Patients With Schizophrenia, Bipolar Disorder or Autism Spectrum Disorder