FAM169A

Summary

FAM169A (family with sequence similarity 169 member A, HGNC:29138) is a protein-coding gene on chromosome 5q13.3, encoding Soluble lamin-associated protein of 75 kDa (Q9Y6X4).

Predicted to be located in nuclear inner membrane.

Source: NCBI Gene 26049 — RefSeq curated summary.

At a glance

• Clinical variants (ClinVar): 96 total
• MANE Select transcript: NM_001376049

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:29138
Approved symbol	FAM169A
Name	family with sequence similarity 169 member A
Location	5q13.3
Locus type	gene with protein product
Status	Approved
Aliases	KIAA0888, SLAP75, SLAP
Ensembl gene	ENSG00000198780
Ensembl biotype	protein_coding
OMIM	615769
Entrez	26049

Gene structure

Transcript identifiers

Ensembl transcripts: 20 — 18 protein_coding, 2 nonsense_mediated_decay

ENST00000389156, ENST00000506954, ENST00000510496, ENST00000510609, ENST00000513277, ENST00000514215, ENST00000687041, ENST00000880931, ENST00000880932, ENST00000880933, ENST00000880934, ENST00000921748, ENST00000921749, ENST00000921750, ENST00000921751, ENST00000921752, ENST00000921753, ENST00000921754, ENST00000921755, ENST00000941597

RefSeq mRNA: 7 — MANE Select: NM_001376049 NM_001376049, NM_001376050, NM_001376051, NM_001376052, NM_001376053, NM_001376054, NM_015566

CCDS: CCDS43330

Canonical transcript exons

ENST00000687041 — 13 exons

Exon	Start	End
ENSE00000893745	74838965	74839050
ENSE00000893746	74840074	74840173
ENSE00001504989	74834426	74834597
ENSE00001739158	74841545	74841679
ENSE00002023863	74866165	74866387
ENSE00003466328	74782931	74783134
ENSE00003471193	74800880	74801030
ENSE00003484782	74813840	74814019
ENSE00003537734	74796030	74796186
ENSE00003607763	74805156	74805284
ENSE00003635886	74801590	74801629
ENSE00003638343	74777574	74782008
ENSE00003672618	74804493	74804605

Expression profiles

Bgee: expression breadth ubiquitous, 217 present calls, max score 99.07.

FANTOM5 (CAGE): breadth broad, TPM avg 5.9807 / max 159.3052, expressed in 865 samples.

FANTOM5 promoters (10 alternative TSS)

Promoter ID	TPM avg	Samples expressed
62097	4.2807	805
62099	0.6650	287
62096	0.4527	246
62102	0.1964	73
62101	0.1841	89
62103	0.1114	48
62098	0.0389	11
62100	0.0335	13
62104	0.0147	3
62094	0.0032	1

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
caput epididymis	UBERON:0004358	99.07	gold quality
corpus epididymis	UBERON:0004359	98.49	gold quality
lateral nuclear group of thalamus	UBERON:0002736	97.36	gold quality
endothelial cell	CL:0000115	96.25	gold quality
postcentral gyrus	UBERON:0002581	95.17	gold quality
cranial nerve II	UBERON:0000941	94.93	gold quality
parietal lobe	UBERON:0001872	94.77	gold quality
entorhinal cortex	UBERON:0002728	94.39	gold quality
substantia nigra pars compacta	UBERON:0001965	93.88	gold quality
superior vestibular nucleus	UBERON:0007227	93.39	gold quality
Brodmann (1909) area 23	UBERON:0013554	93.37	gold quality
substantia nigra pars reticulata	UBERON:0001966	93.23	gold quality
secondary oocyte	CL:0000655	93.04	gold quality
superior frontal gyrus	UBERON:0002661	92.55	gold quality
ventral tegmental area	UBERON:0002691	91.64	gold quality
lateral globus pallidus	UBERON:0002476	91.58	gold quality
pons	UBERON:0000988	91.52	gold quality
corpus callosum	UBERON:0002336	91.44	gold quality
subthalamic nucleus	UBERON:0001906	91.04	gold quality
cauda epididymis	UBERON:0004360	90.98	gold quality
globus pallidus	UBERON:0001875	90.16	gold quality
middle temporal gyrus	UBERON:0002771	90.16	gold quality
dorsal plus ventral thalamus	UBERON:0001897	90.10	gold quality
medial globus pallidus	UBERON:0002477	89.87	gold quality
oocyte	CL:0000023	89.86	gold quality
pigmented layer of retina	UBERON:0001782	88.35	gold quality
inferior vagus X ganglion	UBERON:0005363	88.20	gold quality
occipital lobe	UBERON:0002021	87.89	gold quality
cerebellar vermis	UBERON:0004720	87.59	gold quality
primary visual cortex	UBERON:0002436	87.21	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	no	5.02

Regulation

Is transcription factor: no

Cross-species orthologs

4 orthologs

Organism	Symbol	Gene ID
danio_rerio	fam169ab	ENSDARG00000004177
danio_rerio	fam169aa	ENSDARG00000059719
mus_musculus	Fam169a	ENSMUSG00000041817
rattus_norvegicus	Fam169a	ENSRNOG00000016505

Protein

Protein identifiers

Soluble lamin-associated protein of 75 kDa — Q9Y6X4 (reviewed: Q9Y6X4)

Alternative names: Protein FAM169A

All UniProt accessions (4): Q9Y6X4, D6R953, D6RB01, D6RFI5

UniProt curated annotations — full annotation on UniProt →

Subcellular location. Nucleus envelope. Nucleus inner membrane.

Similarity. Belongs to the FAM169 family.

Isoforms (2)

UniProt ID	Names	Canonical?
Q9Y6X4-1	1	yes
Q9Y6X4-2	2

RefSeq proteins (7): NP_001362978, NP_001362979, NP_001362980, NP_001362981, NP_001362982, NP_001362983, NP_056381 (=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR029625	FAM169	Family

UniProt features (23 total): compositionally biased region 10, modified residue 7, region of interest 2, splice variant 2, chain 1, sequence conflict 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q9Y6X4-F1	61.51	0.33

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 (7): 350, 379, 449, 515, 615, 618, 635

Function

Pathways and Gene Ontology

Reactome pathways

1 pathways

ID	Pathway
R-HSA-9035034	RHOF GTPase cycle

MSigDB gene sets: 153 (showing top): BROWNE_HCMV_INFECTION_30MIN_DN, MODULE_255, GOZGIT_ESR1_TARGETS_DN, MODULE_317, BROWNE_HCMV_INFECTION_16HR_UP, KIM_RESPONSE_TO_TSA_AND_DECITABINE_UP, DACOSTA_UV_RESPONSE_VIA_ERCC3_COMMON_DN, CHIANG_LIVER_CANCER_SUBCLASS_INTERFERON_DN, FLECHNER_BIOPSY_KIDNEY_TRANSPLANT_REJECTED_VS_OK_DN, CHIANG_LIVER_CANCER_SUBCLASS_CTNNB1_UP, GOCC_NUCLEAR_ENVELOPE, YAGI_AML_WITH_11Q23_REARRANGED, GOCC_ORGANELLE_INNER_MEMBRANE, GOCC_NUCLEAR_INNER_MEMBRANE, GOCC_NUCLEAR_MEMBRANE

GO Biological Process (0):

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

GO Cellular Component (4): nuclear inner membrane (GO:0005637), nucleus (GO:0005634), nuclear envelope (GO:0005635), membrane (GO:0016020)

Reactome top-level categories

Rollup of top-1 pathways:

Category	Pathways
RHO GTPase cycle	1

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
binding	1
organelle inner membrane	1
nuclear membrane	1
intracellular membrane-bounded organelle	1
nucleus	1
endomembrane system	1
organelle envelope	1
cellular anatomical structure	1

Protein interactions and networks

STRING

1557 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
FAM169A	LRIT2	A6NDA9	573
FAM169A	CCDC126	Q96EE4	531
FAM169A	BTRC	Q9Y297	531
FAM169A	SEC22C	Q9BRL7	480
FAM169A	WDR17	Q8IZU2	470
FAM169A	GRIFIN	A4D1Z8	454
FAM169A	CLPTM1L	Q96KA5	413
FAM169A	TMEM201	Q5SNT2	366
FAM169A	WDR31	Q8NA23	363
FAM169A	HEATR5B	Q9P2D3	359
FAM169A	ZNF846	Q147U1	358
FAM169A	PPEF2	O14830	345
FAM169A	ACP7	Q6ZNF0	338
FAM169A	TTC23	Q5W5X9	331
FAM169A	DHX32	Q7L7V1	328

IntAct

14 interactions, top by confidence:

A	B	Type	Score
MTMR9	FAM169A	psi-mi:“MI:0915”(physical association)	0.560
LMNB1	FAM169A	psi-mi:“MI:0915”(physical association)	0.560
INHBE	HSPA5	psi-mi:“MI:0914”(association)	0.530
APOA1	CNMD	psi-mi:“MI:0914”(association)	0.350
INHBE	MYO1F	psi-mi:“MI:0914”(association)	0.350
RCOR1	ZBTB5	psi-mi:“MI:0914”(association)	0.350
CANX	ESYT2	psi-mi:“MI:2364”(proximity)	0.270
LMNA	SMCHD1	psi-mi:“MI:2364”(proximity)	0.270
H2BC10	SMCHD1	psi-mi:“MI:2364”(proximity)	0.270
FAM169A	MTMR9	psi-mi:“MI:0915”(physical association)	0.000
LMNB1	FAM169A	psi-mi:“MI:0915”(physical association)	0.000

BioGRID (47): FAM169A (Proximity Label-MS), FAM169A (Affinity Capture-MS), FAM169A (Proximity Label-MS), FAM169A (Proximity Label-MS), FAM169A (Affinity Capture-RNA), FAM169A (Two-hybrid), FAM169A (Two-hybrid), FAM169A (Proximity Label-MS), FAM169A (Proximity Label-MS), FAM169A (Positive Genetic), FAM169A (Proximity Label-MS), FAM169A (Proximity Label-MS), FAM169A (Proximity Label-MS), FAM169A (Proximity Label-MS), FAM169A (Proximity Label-MS)

ESM2 similar proteins: A0A0M3U1B0, A0A1L8EYB2, A0JMF7, A1L2Y1, A2ALV5, A9JRX0, B2GUZ2, D3ZSP7, F1QB81, O35892, O70608, O75113, P23497, P70347, Q0P5X5, Q13129, Q16533, Q2T9I9, Q3U1D0, Q5CZC0, Q5H9M0, Q5REF4, Q5RHB5, Q5SW75, Q5T4T6, Q5T5J6, Q5XG69, Q5ZLE9, Q60664, Q63HN8, Q7M6U3, Q7Z4H7, Q80VH0, Q8BVK9, Q8C263, Q8CCC3, Q8NA03, Q90WN7, Q92844, Q96QP1

Diamond homologs: Q5XG69, Q8CHT6, Q8N8A8, Q9Y6X4

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	78
Likely benign	4
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

2247 predictions. Top by Δscore:

Variant	Effect	Δscore
5:74782004:GGGGT:G	acceptor_gain	1.0000
5:74782007:GT:G	acceptor_gain	1.0000
5:74782007:GTCTG:G	acceptor_loss	1.0000
5:74782009:C:CC	acceptor_gain	1.0000
5:74782927:TTA:T	donor_loss	1.0000
5:74782935:T:C	donor_gain	1.0000
5:74782972:C:CT	donor_gain	1.0000
5:74783130:GATTC:G	acceptor_gain	1.0000
5:74783131:ATTC:A	acceptor_gain	1.0000
5:74783131:ATTCC:A	acceptor_gain	1.0000
5:74783132:TTC:T	acceptor_gain	1.0000
5:74783132:TTCCT:T	acceptor_gain	1.0000
5:74783133:TC:T	acceptor_gain	1.0000
5:74783134:CC:C	acceptor_gain	1.0000
5:74783135:C:CC	acceptor_gain	1.0000
5:74783138:CACCA:C	acceptor_gain	1.0000
5:74783140:CCA:C	acceptor_gain	1.0000
5:74783141:CA:C	acceptor_gain	1.0000
5:74783142:A:AC	acceptor_gain	1.0000
5:74783142:A:C	acceptor_gain	1.0000
5:74783142:A:T	acceptor_gain	1.0000
5:74796027:TACC:T	donor_loss	1.0000
5:74796028:A:AC	donor_gain	1.0000
5:74796029:C:CA	donor_loss	1.0000
5:74796029:C:CC	donor_gain	1.0000
5:74796029:CCTTT:C	donor_gain	1.0000
5:74796030:CTTTT:C	donor_gain	1.0000
5:74796031:TTTTC:T	donor_gain	1.0000
5:74796182:CCAAT:C	acceptor_gain	1.0000
5:74796183:CAAT:C	acceptor_gain	1.0000

AlphaMissense

0 scored. Top likely-pathogenic:

dbSNP variants (sampled 300 via entrez): RS1000044230 (5:74866638 A>T), RS1000050933 (5:74815919 A>G), RS1000067812 (5:74809354 G>A), RS1000147478 (5:74834098 A>T), RS1000154054 (5:74860424 T>A), RS1000191079 (5:74807239 G>A), RS1000194196 (5:74790483 T>G), RS1000242531 (5:74834342 T>C), RS1000245234 (5:74829854 C>T), RS1000270318 (5:74860152 A>G), RS1000369756 (5:74809617 A>C), RS1000404686 (5:74847526 A>G), RS1000405291 (5:74865954 C>A,G), RS1000443454 (5:74809986 G>A), RS1000513508 (5:74853102 C>T)

Disease associations

OMIM: gene MIM:615769 | 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

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

Chemical	Actions (top 5)	PubMed papers
Valproic Acid	affects expression, decreases expression, increases expression	4
Cyclosporine	decreases expression	3
mercuric bromide	increases expression, affects cotreatment	2
Phenylmercuric Acetate	affects cotreatment, increases expression	2
Tetrachlorodibenzodioxin	increases expression, affects expression	2
FR900359	increases phosphorylation	1
triphenyl phosphate	affects expression	1
deoxynivalenol	decreases expression	1
beta-lapachone	decreases expression, increases expression	1
potassium chromate(VI)	increases expression	1
coumarin	decreases phosphorylation	1
S-(1,2-dichlorovinyl)cysteine	affects response to substance, increases expression	1
di-n-butylphosphoric acid	affects expression	1
perfluorooctane sulfonic acid	decreases expression	1
4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamide	affects cotreatment, increases expression	1
clothianidin	increases expression	1
dorsomorphin	affects cotreatment, increases expression	1
jinfukang	decreases expression	1
NSC 689534	affects binding, decreases expression	1
Sunitinib	decreases expression	1
Vorinostat	decreases expression	1
Leflunomide	increases expression	1
Air Pollutants	increases abundance, increases expression	1
Benzo(a)pyrene	decreases methylation, affects methylation	1
Caffeine	affects phosphorylation	1
Copper	affects binding, decreases expression	1
Coumestrol	decreases expression	1
Dimethyl Sulfoxide	increases expression	1
Doxorubicin	decreases expression	1
Endosulfan	decreases expression	1

Clinical trials (associated diseases)

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