FAM156A

Summary

FAM156A (family with sequence similarity 156 member A, HGNC:30114) is a protein-coding gene on chromosome Xp11.22, encoding Protein FAM156A/FAM156B (Q8NDB6).

Predicted to enable methylated histone binding activity. Located in nuclear envelope.

Source: NCBI Gene 29057 — RefSeq curated summary.

At a glance

• Clinical variants (ClinVar): 6 total — 3 pathogenic
• MANE Select transcript: NM_001387706

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:30114
Approved symbol	FAM156A
Name	family with sequence similarity 156 member A
Location	Xp11.22
Locus type	gene with protein product
Status	Approved
Aliases	PRO0659
Ensembl gene	ENSG00000268350
Ensembl biotype	protein_coding
Entrez	29057

Gene structure

Transcript identifiers

Ensembl transcripts: 51 — 45 protein_coding, 5 protein_coding_CDS_not_defined, 1 nonsense_mediated_decay

ENST00000596733, ENST00000610625, ENST00000611661, ENST00000612083, ENST00000612846, ENST00000612915, ENST00000613284, ENST00000615092, ENST00000615171, ENST00000616235, ENST00000616592, ENST00000617970, ENST00000618601, ENST00000619373, ENST00000619518, ENST00000619586, ENST00000619897, ENST00000622197, ENST00000622323, ENST00000622430, ENST00000622447, ENST00000622732, ENST00000623782, ENST00000910138, ENST00000910139, ENST00000910140, ENST00000910141, ENST00000910142, ENST00000910143, ENST00000910144, ENST00000910145, ENST00000910146, ENST00000919360, ENST00000919361, ENST00000919362, ENST00000919363, ENST00000956877, ENST00000956878, ENST00000956879, ENST00000956880, ENST00000956881, ENST00000956882, ENST00000956883, ENST00000956884, ENST00000956885, ENST00000956886, ENST00000956887, ENST00000956888, ENST00000956889, ENST00000956890, ENST00000956891

RefSeq mRNA: 15 — MANE Select: NM_001387706 NM_001242489, NM_001242490, NM_001242491, NM_001242492, NM_001242493, NM_001242494, NM_001242495, NM_001242496, NM_001242497, NM_001377060, NM_001377061, NM_001377062, NM_001377063, NM_001387706, NM_014138

CCDS: CCDS35297

Canonical transcript exons

ENST00000622447 — 3 exons

Exon	Start	End
ENSE00003013760	52955154	52955246
ENSE00003739566	52956273	52958518
ENSE00003741620	52947254	52948705

Expression profiles

Bgee: expression breadth ubiquitous, 134 present calls, max score 92.74.

FANTOM5 (CAGE): breadth broad, TPM avg 1.5117 / max 19.9269, expressed in 907 samples.

FANTOM5 promoters (3 alternative TSS)

Promoter ID	TPM avg	Samples expressed
199316	1.0146	583
209706	0.5680	304
199315	0.4970	284

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
pituitary gland	UBERON:0000007	92.74	gold quality
right hemisphere of cerebellum	UBERON:0014890	92.40	gold quality
cerebellar cortex	UBERON:0002129	91.87	gold quality
cerebellum	UBERON:0002037	91.82	gold quality
cerebellar hemisphere	UBERON:0002245	91.80	gold quality
adenohypophysis	UBERON:0002196	91.76	gold quality
apex of heart	UBERON:0002098	90.14	gold quality
descending thoracic aorta	UBERON:0002345	89.58	gold quality
placenta	UBERON:0001987	89.14	gold quality
tibial nerve	UBERON:0001323	89.02	gold quality
right adrenal gland cortex	UBERON:0035827	89.01	gold quality
cortex of kidney	UBERON:0001225	88.53	gold quality
right adrenal gland	UBERON:0001233	88.52	gold quality
thoracic aorta	UBERON:0001515	88.36	gold quality
ascending aorta	UBERON:0001496	88.29	gold quality
right ovary	UBERON:0002118	88.17	gold quality
mucosa of stomach	UBERON:0001199	88.16	gold quality
left coronary artery	UBERON:0001626	88.06	gold quality
skin of abdomen	UBERON:0001416	88.04	gold quality
left adrenal gland cortex	UBERON:0035825	88.01	gold quality
metanephros cortex	UBERON:0010533	87.96	gold quality
subcutaneous adipose tissue	UBERON:0002190	87.75	gold quality
left ovary	UBERON:0002119	87.73	gold quality
zone of skin	UBERON:0000014	87.72	gold quality
skin of leg	UBERON:0001511	87.62	gold quality
left adrenal gland	UBERON:0001234	87.61	gold quality
right coronary artery	UBERON:0001625	87.60	gold quality
body of uterus	UBERON:0009853	87.48	gold quality
endocervix	UBERON:0000458	87.34	gold quality
superior frontal gyrus	UBERON:0002661	87.24	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-MTAB-6701	yes	46.52
E-ANND-3	yes	3.99

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

18 targeting FAM156A, 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-5002-5P	99.76	70.84	1763
HSA-MIR-5004-5P	99.68	66.63	1294
HSA-MIR-3202	99.66	67.70	2737
HSA-MIR-3685	99.62	68.83	1621
HSA-MIR-7152-5P	99.60	69.33	2094
HSA-MIR-888-3P	99.53	69.77	1057
HSA-MIR-4672	99.50	71.58	2893
HSA-MIR-7515	99.31	68.22	1795
HSA-MIR-155-3P	99.03	67.99	924
HSA-MIR-3619-5P	99.00	68.87	2308
HSA-MIR-4751	98.80	64.95	525
HSA-MIR-214-3P	98.71	68.12	2128
HSA-MIR-761	98.71	68.07	2051
HSA-MIR-9500	98.62	66.54	1845
HSA-MIR-7112-3P	97.67	68.77	948
HSA-MIR-3928-3P	97.61	66.53	1096
HSA-MIR-5681B	94.82	69.30	514
HSA-MIR-2277-3P	91.94	62.27	299

Cross-species orthologs

2 orthologs

Organism	Symbol	Gene ID
mus_musculus	Vcf2	ENSMUSG00000041353
rattus_norvegicus	Vcf2	ENSRNOG00000090943

Paralogs (1): FAM156B (ENSG00000179304)

Protein

Protein identifiers

Protein FAM156A/FAM156B — Q8NDB6 (reviewed: Q8NDB6)

Alternative names: Transmembrane protein 29/29B

All UniProt accessions (9): Q8NDB6, A0A087WTI8, A0A087WVC3, A0A087WVC8, A0A087WY72, A0A087WZD0, A0A087WZZ1, A0A087X275, A0A087X2G5

UniProt curated annotations — full annotation on UniProt →

Subcellular location. Membrane.

RefSeq proteins (15): NP_001229418, NP_001229419, NP_001229420, NP_001229421, NP_001229422, NP_001229423, NP_001229424, NP_001229425, NP_001229426, NP_001363989, NP_001363990, NP_001363991, NP_001363992, NP_001374635, NP_054857 (=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR029096	Dppa3	Family

Pfam: PF15549

UniProt features (13 total): sequence conflict 5, region of interest 2, compositionally biased region 2, modified residue 2, chain 1, transmembrane region 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q8NDB6-F1	68.68	0.18

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): 1, 114

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 55 (showing top): STAEGE_EWING_FAMILY_TUMOR, IZADPANAH_STEM_CELL_ADIPOSE_VS_BONE_UP, GOCC_NUCLEAR_ENVELOPE, LEIN_MIDBRAIN_MARKERS, LEIN_PONS_MARKERS, LEIN_MEDULLA_MARKERS, GOCC_ORGANELLE_ENVELOPE, chrXp11, ZWANG_DOWN_BY_2ND_EGF_PULSE, GCM_RAB10, GSE14699_NAIVE_VS_ACT_CD8_TCELL_UP, ASH1L_TARGET_GENES, CEBPZ_TARGET_GENES, E2F2_TARGET_GENES, FOXD2_TARGET_GENES

GO Biological Process (0):

GO Molecular Function (2): protein binding (GO:0005515), obsolete methylated histone binding (GO:0035064)

GO Cellular Component (2): nuclear envelope (GO:0005635), membrane (GO:0016020)

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
binding	1
nucleus	1
endomembrane system	1
organelle envelope	1
cellular anatomical structure	1

Protein interactions and networks

STRING

174 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
FAM156A	RBM41	Q96IZ5	456
FAM156A	TMEM164	Q5U3C3	444
FAM156A	DYDC2	Q96IM9	380
FAM156A	NME6	O75414	370
FAM156A	PPP1R3F	Q6ZSY5	369
FAM156A	GOLGA8B	A8MQT2	358
FAM156A	GNB4	Q9HAV0	348
FAM156A	MRPS25	P82663	348
FAM156A	DEF8	Q6ZN54	348
FAM156A	GALNT16	Q8N428	348
FAM156A	RBM33	Q96EV2	348
FAM156A	CCDC14	Q49A88	348
FAM156A	TMEM106A	Q96A25	348
FAM156A	DNAAF6	Q9NQM4	336
FAM156A	GAB3	Q8WWW8	328

IntAct

21 interactions, top by confidence:

A	B	Type	Score
SAT1	FAM156B	psi-mi:“MI:0915”(physical association)	0.560
TEX11	FAM156B	psi-mi:“MI:0915”(physical association)	0.560
ATRIP	FAM156B	psi-mi:“MI:0915”(physical association)	0.560
FAM156B	TFIP11	psi-mi:“MI:0915”(physical association)	0.560
FAM156B	SAT1	psi-mi:“MI:0915”(physical association)	0.560
FAM156B	TEX11	psi-mi:“MI:0915”(physical association)	0.560
TFIP11	FAM156B	psi-mi:“MI:0915”(physical association)	0.560
FAM156B	CRACR2A	psi-mi:“MI:0915”(physical association)	0.560
GADD45G	FAM156B	psi-mi:“MI:0915”(physical association)	0.560
FAM156B	PB2	psi-mi:“MI:0915”(physical association)	0.370
MAGEA11	FAM156B	psi-mi:“MI:0915”(physical association)	0.370
CRACR2A	FAM156B	psi-mi:“MI:0915”(physical association)	0.000
GADD45G	FAM156B	psi-mi:“MI:0915”(physical association)	0.000

BioGRID (10): FAM156A (Two-hybrid), FAM156A (Two-hybrid), TEX11 (Two-hybrid), ATRIP (Two-hybrid), FAM156A (Two-hybrid), FAM156B (Two-hybrid), FAM156A (Two-hybrid), FAM156B (Two-hybrid), FAM156A (Two-hybrid), FAM156A (Affinity Capture-RNA)

ESM2 similar proteins: A0A1B0GVQ3, A0A1W2PPK0, A0A1W2PPM1, A2A9I7, A6NCI8, A6QQS3, A7XCE8, E9PI22, E9PXT9, O15016, O91083, P09414, P0DMB1, P17923, P18804, P20879, P35965, P49750, Q0P670, Q12857, Q1RMX6, Q32LN6, Q32MG2, Q3B8N5, Q3T016, Q3V0A6, Q4JK59, Q5BI31, Q5T035, Q5ZKH6, Q642A3, Q6AXV6, Q6IMN6, Q6P1W5, Q6PEX7, Q6X4T0, Q80YD3, Q86UF4, Q8BII1, Q8C5V0

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	3
Likely pathogenic	0
Uncertain significance	2
Likely benign	0
Benign	0

Top pathogenic / likely-pathogenic (3)

Variant ID	HGVS	Classification
3391954	GRCh37/hg19 Xp11.22(chrX:52677621-53324469)x1	Pathogenic
545551	NC_000023.10:g.36649710_136649711del100000002insG	Pathogenic
933150	GRCh37/hg19 Xp11.22(chrX:52923471-53765589)x2	Pathogenic

SpliceAI

871 predictions. Top by Δscore:

Variant	Effect	Δscore
X:52958361:T:A	donor_gain	1.0000
X:52958362:C:CA	donor_gain	1.0000
X:52948701:CCAGA:C	acceptor_gain	0.9900
X:52948702:CAGA:C	acceptor_gain	0.9900
X:52948702:CAGAC:C	acceptor_gain	0.9900
X:52948703:AGA:A	acceptor_gain	0.9900
X:52948704:GA:G	acceptor_gain	0.9900
X:52948706:C:CC	acceptor_gain	0.9900
X:52948712:C:CT	acceptor_gain	0.9900
X:52948714:CAAGG:C	acceptor_gain	0.9900
X:52948718:G:C	acceptor_gain	0.9900
X:52948718:G:GC	acceptor_gain	0.9900
X:52958273:C:CA	donor_gain	0.9900
X:52958355:A:AC	donor_gain	0.9900
X:52958381:T:A	donor_gain	0.9900
X:52958404:CG:C	donor_gain	0.9900
X:52958404:CGCG:C	donor_gain	0.9900
X:52948704:GACTG:G	acceptor_loss	0.9800
X:52948705:ACTG:A	acceptor_loss	0.9800
X:52948715:A:T	acceptor_gain	0.9800
X:52948721:A:AC	acceptor_gain	0.9800
X:52948721:A:C	acceptor_gain	0.9800
X:52952368:TTAC:T	donor_gain	0.9800
X:52958297:T:TA	donor_gain	0.9800
X:52958346:C:A	donor_gain	0.9800
X:52958377:G:A	donor_gain	0.9800
X:52958403:A:AC	donor_gain	0.9800
X:52958404:C:CC	donor_gain	0.9800
X:52948710:A:T	acceptor_gain	0.9700
X:52952367:TTTA:T	donor_gain	0.9700

AlphaMissense

0 scored. Top likely-pathogenic:

dbSNP variants (sampled 300 via entrez): RS1000852985 (X:52983576 A>G), RS1001036997 (X:52992968 G>A), RS1001367803 (X:52977109 T>C), RS1001448265 (X:52993661 C>T), RS1001526281 (X:52988562 A>T), RS1001694196 (X:52997463 G>A,T), RS1001852886 (X:52986074 C>T), RS1001903753 (X:52986571 A>G), RS1002046244 (X:52995730 C>A,G), RS1002576620 (X:52991201 T>C), RS1004397207 (X:52984714 C>G), RS1004659613 (X:52983036 G>A,T), RS1005327459 (X:52988021 C>T), RS1005400947 (X:52987501 A>G), RS1005549210 (X:52996937 T>C)

Disease associations

OMIM: gene `` | disease phenotypes: MIM:306955

GenCC curated gene-disease

Mondo (2): heterotaxy, visceral, 1, X-linked (MONDO:0010607), intellectual disability (MONDO:0001071)

Orphanet (2): Visceral heterotaxy (Orphanet:450), NON RARE IN EUROPE: Unexplained intellectual disability (Orphanet:319658)

HPO phenotypes

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

GWAS associations

0 associations (top):

MeSH disease descriptors (2)

Descriptor	Name	Tree numbers
D008607	Intellectual Disability	C10.597.606.360; C23.888.592.604.646; F01.700.687; F03.625.539
C538116	Heterotaxy, visceral, X-linked (supp.)

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

30 total (human), top 30 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
FR900359	decreases phosphorylation	1
bisphenol F	affects cotreatment, decreases expression	1
beta-lapachone	decreases expression	1
tris(1,3-dichloro-2-propyl)phosphate	decreases expression	1
butyraldehyde	decreases expression	1
zinc chromate	decreases expression, increases abundance	1
chromium hexavalent ion	decreases expression, increases abundance	1
CGP 52608	affects binding, increases reaction	1
abrine	decreases expression	1
bisphenol S	increases expression	1
Air Pollutants	affects expression, increases abundance	1
Arsenic	increases methylation	1
Calcitriol	affects cotreatment, decreases expression	1
Dexamethasone	affects cotreatment, decreases expression	1
Dimethyl Sulfoxide	increases expression	1
Estradiol	increases expression	1
Hydralazine	increases expression, affects cotreatment	1
Hydrogen Peroxide	affects expression	1
Indomethacin	affects cotreatment, decreases expression	1
Ozone	affects expression, increases abundance	1
Testosterone	decreases expression, affects cotreatment	1
Tretinoin	decreases expression	1
Urethane	decreases expression	1
Valproic Acid	affects cotreatment, increases expression	1
1-Methyl-3-isobutylxanthine	affects cotreatment, decreases expression	1
Cyclosporine	increases methylation	1
Okadaic Acid	decreases expression	1
Copper Sulfate	decreases expression	1
Vitamin K 3	affects expression	1
Particulate Matter	increases expression	1

Clinical trials (associated diseases)

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

Trial	Phase	Status	Title
NCT05657860	PHASE4	COMPLETED	Guanfacine Extended Release for the Reduction of Aggression and Self-injurious Behavior Associated With Prader-Willi Syndrome
NCT05744479	PHASE4	RECRUITING	Metformin for Antipsychotic-induced Weight Gain in Adults With Intellectual Disability
NCT06107829	PHASE4	WITHDRAWN	Valbenazine Treatment of Tardive Dyskinesia in Adults With Intellectual/Developmental Disabilities
NCT06997198	PHASE4	NOT_YET_RECRUITING	Deutetrabenazine Treatment for Tardive Dyskinesia in Intellectual/Developmental Disabilities
NCT02270736	PHASE3	COMPLETED	Clinical Study to Investigate the Efficacy and Safety of NT 201 Compared to Placebo in the Treatment of Chronic Troublesome Drooling Associated With Neurological Disorders and/or Intellectual Disability
NCT02304302	PHASE2	COMPLETED	Down Syndrome Memantine Follow-up Study
NCT03862950	PHASE2	COMPLETED	A Trial of Metformin in Individuals With Fragile X Syndrome (Met)
NCT04529226	PHASE2	UNKNOWN	Study to Compare Clozapine vs Treatment as Usual in People With Intellectual Disability & Treatment-resistant Psychosis
NCT04821856	PHASE2	COMPLETED	Evaluation of the Effectiveness of Cannabidiol in Treating Severe Behavioural Problems in Children and Adolescents With Intellectual Disability
NCT05273320	PHASE1	COMPLETED	Clinical Trial of Nabilone for Aggression in Adults With Intellectual and Developmental Disabilities
NCT05301361	PHASE1	ENROLLING_BY_INVITATION	Sensitivity of the NIH Toolbox to Stimulant Treatment in Intellectual Disabilities
NCT06016764	PHASE1	COMPLETED	Use of MRI and cTBS for Catatonia in Autism
NCT06586827	PHASE1	COMPLETED	Impact of Competency-Based Training and Technical Assistance Employment Outcomes of Individuals With ID/DD
NCT07531940	PHASE1	NOT_YET_RECRUITING	Escalating Doses of Memantine in Down Syndrome (MEDS-123)
NCT03479476	PHASE2/PHASE3	COMPLETED	A Trial of Metformin in Individuals With Fragile X Syndrome
NCT02616796	PHASE1/PHASE2	COMPLETED	Effects of Social Gaze Training on Brain and Behavior in Fragile X Syndrome
NCT06860672	EARLY_PHASE1	RECRUITING	Clinical Trial of the Dual Vector Base Editor for the Treatment of the CHD3-R1025W Mutation
NCT00597948	Not specified	COMPLETED	Healthy Lifestyles for People With Intellectual Disabilities
NCT01087320	Not specified	RECRUITING	Genome Medical Sequencing for Gene Discovery
NCT01652963	Not specified	UNKNOWN	Picture-based Computerised Assessment and Training of Cognitive Behaviour Therapy Skills
NCT01695395	Not specified	COMPLETED	Mental Health Care Provision for Adults With Intellectual Disability and a Mental Disorder
NCT01867554	Not specified	COMPLETED	Research and Characterization of New Genes Involved in Intellectual Disability
NCT01915381	Not specified	COMPLETED	Improving Adherence Healthy Lifestyle With a Smartphone Application Based on Adults With Intellectual Disabilities
NCT01988623	Not specified	COMPLETED	Pivotal Response Treatment for Individuals With Intellectual Disabilities
NCT02099773	Not specified	COMPLETED	Support Staff-client Interactions With Augmentative and Alternative Communication
NCT02136849	Not specified	COMPLETED	Inter-regional Project of the Great Western Exploration Approach for Exome Molecular Causes Severe Intellectual Disability Isolated or Syndromic
NCT02225041	Not specified	COMPLETED	Sedation Strategy and Cognitive Outcome After Critical Illness in Early Childhood
NCT02414438	Not specified	COMPLETED	Establishing the Clinical Utility of First StepDx PLUS and NextStepDx PLUS Study
NCT02451761	Not specified	COMPLETED	Apparently Balanced Chromosomal Translocation/ Next-generation Sequencing/ Intellectual Disability
NCT02461420	Not specified	ACTIVE_NOT_RECRUITING	Mapping the Genotype, Phenotype, and Natural History of Phelan-McDermid Syndrome
NCT02461459	Not specified	ACTIVE_NOT_RECRUITING	Autism Spectrum Disorder (ASD) and Intellectual Disability (ID) Determinants in Tuberous Sclerosis Complex (TSC)
NCT02486081	Not specified	COMPLETED	Development and Application-Smart Football for Movement Evaluation and Training in the Special Education Population
NCT02504502	Not specified	COMPLETED	Enhancing Genomic Laboratory Reports to Enhance Communication and Empower Patients
NCT02513277	Not specified	COMPLETED	Diabetes Screening & Prevention for People With Learning (Intellectual) Disabilities:STOP Diabetes Study
NCT02561754	Not specified	COMPLETED	Weight Management for Adolescents With IDD
NCT02591446	Not specified	COMPLETED	Transcranial Magnetic Stimulation Studies in Autism Spectrum Disorders
NCT02714868	Not specified	COMPLETED	Evaluation of Project TEAM (Teens Making Environmental and Activity Modifications)
NCT02721394	Not specified	UNKNOWN	FCT With Young Children With ID in the UK: A Feasibility Project V.1
NCT02746614	Not specified	COMPLETED	Psychomotor Therapy Effects in Adaptive Behavior and Motor Proficiency in Intellectual Disability
NCT02836405	Not specified	COMPLETED	TMS for the Investigation of Brain Plasticity in Autism Spectrum Disorders