FAM170B

Summary

FAM170B (family with sequence similarity 170 member B, HGNC:19736) is a protein-coding gene on chromosome 10q11.23, encoding Protein FAM170B (A6NMN3). Plays a role in fertilization through the acrosome reaction.

Predicted to be involved in fertilization; positive regulation of acrosome reaction; and regulation of fertilization. Located in acrosomal vesicle.

Source: NCBI Gene 170370 — RefSeq curated summary.

At a glance

• GWAS associations: 1
• Clinical variants (ClinVar): 54 total — 1 pathogenic
• MANE Select transcript: NM_001164484

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:19736
Approved symbol	FAM170B
Name	family with sequence similarity 170 member B
Location	10q11.23
Locus type	gene with protein product
Status	Approved
Aliases	AC084727.4
Ensembl gene	ENSG00000172538
Ensembl biotype	protein_coding
Entrez	170370

Gene structure

Transcript identifiers

Ensembl transcripts: 1 — 1 protein_coding

ENST00000311787

RefSeq mRNA: 1 — MANE Select: NM_001164484 NM_001164484

CCDS: CCDS53536

Canonical transcript exons

ENST00000311787 — 2 exons

Exon	Start	End
ENSE00001189720	49131154	49132352
ENSE00001189727	49133807	49134021

Expression profiles

Bgee: expression breadth broad, 14 present calls, max score 92.75.

Top tissues by expression

215 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	92.75	gold quality
sperm	CL:0000019	74.41	gold quality
buccal mucosa cell	CL:0002336	72.85	gold quality
left testis	UBERON:0004533	65.36	gold quality
right testis	UBERON:0004534	65.03	gold quality
testis	UBERON:0000473	63.53	gold quality
tendon of biceps brachii	UBERON:0008188	54.30	gold quality
medial globus pallidus	UBERON:0002477	49.64	gold quality
globus pallidus	UBERON:0001875	47.51	gold quality
lower lobe of lung	UBERON:0008949	45.38	silver quality
adult organism	UBERON:0007023	44.58	gold quality
amniotic fluid	UBERON:0000173	44.49	gold quality
skeletal muscle tissue of rectus abdominis	UBERON:0004511	43.37	gold quality
secondary oocyte	CL:0000655	42.57	gold quality
vastus lateralis	UBERON:0001379	41.73	gold quality
quadriceps femoris	UBERON:0001377	41.69	gold quality
superficial temporal artery	UBERON:0001614	41.33	gold quality
palpebral conjunctiva	UBERON:0001812	41.10	gold quality
mucosa of paranasal sinus	UBERON:0005030	40.98	gold quality
subthalamic nucleus	UBERON:0001906	40.85	gold quality
jejunal mucosa	UBERON:0000399	40.59	gold quality
biceps brachii	UBERON:0001507	40.57	gold quality
skeletal muscle tissue	UBERON:0001134	40.54	gold quality
epithelium of nasopharynx	UBERON:0001951	40.45	gold quality
myocardium	UBERON:0002349	40.45	gold quality
gingival epithelium	UBERON:0001949	40.43	gold quality
germinal epithelium of ovary	UBERON:0001304	40.33	gold quality
esophagus squamous epithelium	UBERON:0006920	40.29	gold quality
skeletal muscle tissue of biceps brachii	UBERON:0004502	40.27	gold quality
jejunum	UBERON:0002115	40.18	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	no	0.64

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

47 targeting FAM170B, 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-3689D	100.00	66.14	1181
HSA-MIR-6851-5P	100.00	65.63	1294
HSA-MIR-6759-5P	99.99	66.54	785
HSA-MIR-6793-5P	99.97	65.95	758
HSA-MIR-4725-3P	99.96	69.53	2520
HSA-MIR-6780B-5P	99.96	69.60	2562
HSA-MIR-6721-5P	99.93	68.92	2981
HSA-MIR-1297	99.91	73.41	3162
HSA-MIR-4492	99.87	68.25	3611
HSA-MIR-3121-3P	99.82	71.96	3630
HSA-MIR-26A-5P	99.78	73.52	2303
HSA-MIR-26B-5P	99.78	73.51	2305
HSA-MIR-3617-5P	99.75	69.41	1968
HSA-MIR-641	99.75	69.35	1975
HSA-MIR-4465	99.71	72.56	2096
HSA-MIR-6892-3P	99.68	66.40	1178
HSA-MIR-425-5P	99.59	67.67	900
HSA-MIR-762	99.58	66.61	1994
HSA-MIR-3942-3P	99.57	69.03	2854
HSA-MIR-203A-3P	99.49	70.56	2806
HSA-MIR-4498	99.47	67.42	2360
HSA-MIR-6839-3P	99.39	68.86	1301
HSA-MIR-3606-5P	99.31	69.67	1168
HSA-MIR-2054	99.20	68.89	1699
HSA-MIR-5001-5P	99.05	66.76	1972
HSA-MIR-3190-5P	98.87	64.89	1345
HSA-MIR-760	98.81	66.65	1392
HSA-MIR-629-5P	98.78	68.72	1032
HSA-MIR-4763-5P	98.75	63.89	854
HSA-MIR-3945	98.68	64.21	553

Literature-anchored findings (GeneRIF, showing 1)

• Knockout of family with sequence similarity 170 member A (Fam170a) causes male subfertility, while Fam170b is dispensable in micedagger. (PMID:32588889)

Cross-species orthologs

2 orthologs

Organism	Symbol	Gene ID
mus_musculus	Fam170b	ENSMUSG00000078127
rattus_norvegicus	Fam170b	ENSRNOG00000020077

Protein

Protein identifiers

Protein FAM170B — A6NMN3 (reviewed: A6NMN3)

Alternative names: Acrosome-related protein

All UniProt accessions (1): A6NMN3

UniProt curated annotations — full annotation on UniProt →

Function. Plays a role in fertilization through the acrosome reaction.

Subunit / interactions. Interacts with GOPC.

Subcellular location. Cytoplasmic vesicle. Secretory vesicle. Acrosome. Acrosome outer membrane.

Tissue specificity. Exclusively expressed in adult testis.

Similarity. Belongs to the FAM170 family.

RefSeq proteins (1): NP_001157956* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR040879	Spt46-like	Family

Pfam: PF17734

UniProt features (6 total): region of interest 2, chain 1, compositionally biased region 1, sequence variant 1, sequence conflict 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-A6NMN3-F1	61.96	0.24

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 57 (showing top): GOBP_SINGLE_FERTILIZATION, GOBP_POSITIVE_REGULATION_OF_REPRODUCTIVE_PROCESS, GOCC_SECRETORY_GRANULE, GOBP_REGULATION_OF_REPRODUCTIVE_PROCESS, GOBP_REGULATION_OF_ACROSOME_REACTION, GOBP_ACROSOME_REACTION, GOBP_FERTILIZATION, ACEVEDO_LIVER_CANCER_WITH_H3K27ME3_DN, GOCC_ACROSOMAL_MEMBRANE, GOCC_SECRETORY_VESICLE, GOCC_SECRETORY_GRANULE_MEMBRANE, GOCC_ACROSOMAL_VESICLE, GOBP_REGULATION_OF_FERTILIZATION, GSE13522_CTRL_VS_T_CRUZI_Y_STRAIN_INF_SKIN_129_MOUSE_UP, GOBP_POSITIVE_REGULATION_OF_ACROSOME_REACTION

GO Biological Process (3): fertilization (GO:0009566), regulation of fertilization (GO:0080154), positive regulation of acrosome reaction (GO:2000344)

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

GO Cellular Component (4): acrosomal vesicle (GO:0001669), outer acrosomal membrane (GO:0002081), membrane (GO:0016020), cytoplasmic vesicle (GO:0031410)

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
sexual reproduction	1
reproductive process	1
fertilization	1
regulation of reproductive process	1
acrosome reaction	1
regulation of acrosome reaction	1
positive regulation of reproductive process	1
binding	1
secretory granule	1
acrosomal membrane	1
cytoplasmic vesicle membrane	1
cellular anatomical structure	1
cytoplasm	1
intracellular vesicle	1

Protein interactions and networks

STRING

1195 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
FAM170B	WIPF3	A6NGB9	563
FAM170B	SSMEM1	Q8WWF3	526
FAM170B	PRSS55	Q6UWB4	497
FAM170B	EQTN	Q9NQ60	486
FAM170B	TSSK4	Q6SA08	482
FAM170B	CWF19L2	Q2TBE0	480
FAM170B	IQCF1	Q8N6M8	476
FAM170B	PRSS37	A4D1T9	456
FAM170B	LRRC18	Q8N456	451
FAM170B	FSIP2	Q5CZC0	447
FAM170B	HEATR5A	Q86XA9	447
FAM170B	FAM186A	A6NE01	446
FAM170B	TMPRSS12	Q86WS5	438
FAM170B	CIB4	A0PJX0	433
FAM170B	CAPZA3	Q96KX2	427

IntAct

0 interactions, top by confidence:

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

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

Classification	Count (floor)
Pathogenic	1
Likely pathogenic	0
Uncertain significance	46
Likely benign	7
Benign	0

Top pathogenic / likely-pathogenic (1)

Variant ID	HGVS	Classification
563791	GRCh37/hg19 10q11.22-11.23(chr10:46287821-51861565)x1	Pathogenic

SpliceAI

141 predictions. Top by Δscore:

Variant	Effect	Δscore
10:49133802:CCTA:C	donor_loss	1.0000
10:49133803:CTACC:C	donor_loss	1.0000
10:49133806:C:CA	donor_loss	1.0000
10:49133806:CCTGG:C	donor_gain	0.9900
10:49133830:T:A	donor_gain	0.9900
10:49132351:CC:C	acceptor_gain	0.9800
10:49132352:CC:C	acceptor_gain	0.9800
10:49133821:T:TA	donor_gain	0.9800
10:49132350:TCC:T	acceptor_gain	0.9700
10:49132351:CCC:C	acceptor_gain	0.9700
10:49132353:C:CC	acceptor_gain	0.9700
10:49133801:ACCT:A	donor_loss	0.9700
10:49133805:A:AC	donor_gain	0.9700
10:49133806:C:CC	donor_gain	0.9700
10:49132349:GTCC:G	acceptor_gain	0.9600
10:49132348:AGTCC:A	acceptor_gain	0.9500
10:49132349:GTCCC:G	acceptor_gain	0.9500
10:49132350:TCCCT:T	acceptor_gain	0.9500
10:49133803:CT:C	donor_gain	0.9400
10:49133804:TA:T	donor_gain	0.9400
10:49132351:CCCTG:C	acceptor_gain	0.8900
10:49132355:G:C	acceptor_loss	0.8900
10:49133802:CCT:C	donor_gain	0.8600
10:49133805:A:T	donor_gain	0.8300
10:49133800:CACCT:C	donor_gain	0.8200
10:49133801:ACCTA:A	donor_gain	0.8200
10:49133821:TCC:T	donor_gain	0.8200
10:49132664:A:C	donor_gain	0.7800
10:49132353:C:T	acceptor_gain	0.7700
10:49132361:C:CT	acceptor_gain	0.7600

AlphaMissense

1865 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
10:49131772:G:C	F231L	0.979
10:49131772:G:T	F231L	0.979
10:49131774:A:G	F231L	0.979
10:49132078:G:C	F129L	0.962
10:49132078:G:T	F129L	0.962
10:49132080:A:G	F129L	0.962
10:49132036:G:C	F143L	0.953
10:49132036:G:T	F143L	0.953
10:49132038:A:G	F143L	0.953
10:49131757:A:C	F236L	0.946
10:49131757:A:T	F236L	0.946
10:49131759:A:G	F236L	0.946
10:49131769:G:C	S232R	0.942
10:49131769:G:T	S232R	0.942
10:49131771:T:G	S232R	0.942
10:49132098:A:G	W123R	0.929
10:49132098:A:T	W123R	0.929
10:49131754:A:C	F237L	0.912
10:49131754:A:T	F237L	0.912
10:49131756:A:G	F237L	0.912
10:49132096:C:A	W123C	0.899
10:49132096:C:G	W123C	0.899
10:49132052:A:G	I138T	0.885
10:49132003:G:C	F154L	0.878
10:49132003:G:T	F154L	0.878
10:49132005:A:G	F154L	0.878
10:49132137:A:C	Y110D	0.874
10:49131773:A:G	F231S	0.869
10:49132037:A:G	F143S	0.864
10:49131770:C:T	S232N	0.856

dbSNP variants (sampled 300 via entrez): RS1001928647 (10:49135450 A>G), RS1001937976 (10:49134640 C>T), RS1002098928 (10:49130985 A>C,G), RS1002372918 (10:49135272 G>A), RS1003978817 (10:49135754 A>G), RS1004883162 (10:49134639 A>G), RS1004887914 (10:49132275 T>C), RS1005221614 (10:49133530 T>C), RS1005888372 (10:49133709 A>G,T), RS1006783281 (10:49134351 G>A), RS1007008546 (10:49132728 C>A,T), RS1008120035 (10:49135931 A>G), RS1008510343 (10:49135021 C>A,T), RS1008686656 (10:49131393 C>T), RS1008728301 (10:49135224 G>A,T)

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

1 associations (top):

Study	Trait	p-value
GCST010703_114	Brain morphology (MOSTest)	8.000000e-19

EFO canonical traits (1, from GWAS)

EFO ID	Trait name
EFO:0004346	neuroimaging measurement

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

7 total (human), top 7 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
bisphenol A	decreases methylation	1
Resveratrol	affects cotreatment, decreases expression	1
Benzo(a)pyrene	affects methylation, increases methylation	1
Formaldehyde	decreases expression	1
Plant Extracts	affects cotreatment, decreases expression	1
Valproic Acid	increases methylation	1
Aflatoxin B1	increases methylation	1

Clinical trials (associated diseases)

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