FAM47C

Summary

FAM47C (family with sequence similarity 47 member C, HGNC:25301) is a protein-coding gene on chromosome Xp21.1, encoding Putative protein FAM47C (Q5HY64).

This gene encodes a product belonging to a family of proteins with unknown function. The coding sequence of this family member includes several tandemly repeated regions.

Source: NCBI Gene 442444 — RefSeq curated summary.

At a glance

• Gene–disease (curated): male infertility with azoospermia or oligozoospermia due to single gene mutation (Moderate, GenCC)
• Clinical variants (ClinVar): 164 total — 1 pathogenic
• MANE Select transcript: NM_001013736

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:25301
Approved symbol	FAM47C
Name	family with sequence similarity 47 member C
Location	Xp21.1
Locus type	gene with protein product
Status	Approved
Ensembl gene	ENSG00000198173
Ensembl biotype	protein_coding
OMIM	301067
Entrez	442444

Gene structure

Transcript identifiers

Ensembl transcripts: 1 — 1 protein_coding

ENST00000358047

RefSeq mRNA: 1 — MANE Select: NM_001013736 NM_001013736

CCDS: CCDS35227

Canonical transcript exons

ENST00000358047 — 1 exons

Exon	Start	End
ENSE00001412151	37008366	37011664

Expression profiles

Bgee: expression breadth tissue_specific, 10 present calls, max score 85.98.

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
sperm	CL:0000019	85.98	gold quality
adult organism	UBERON:0007023	66.86	gold quality
cardiac muscle of right atrium	UBERON:0003379	56.17	gold quality
testis	UBERON:0000473	56.07	gold quality
left testis	UBERON:0004533	55.81	gold quality
right testis	UBERON:0004534	55.58	gold quality
kidney epithelium	UBERON:0004819	55.52	gold quality
amniotic fluid	UBERON:0000173	55.31	gold quality
left ventricle myocardium	UBERON:0006566	54.23	gold quality
epithelial cell of pancreas	CL:0000083	53.73	gold quality
upper arm skin	UBERON:0004263	53.52	gold quality
nasal cavity epithelium	UBERON:0005384	52.86	gold quality
pancreatic ductal cell	CL:0002079	52.42	silver quality
tibialis anterior	UBERON:0001385	51.15	silver quality
myocardium	UBERON:0002349	51.03	gold quality
deltoid	UBERON:0001476	50.95	gold quality
substantia nigra pars reticulata	UBERON:0001966	50.42	gold quality
lower lobe of lung	UBERON:0008949	49.95	silver quality
ileal mucosa	UBERON:0000331	49.89	silver quality
skin of hip	UBERON:0001554	49.11	silver quality
quadriceps femoris	UBERON:0001377	47.42	gold quality
vastus lateralis	UBERON:0001379	45.65	gold quality
layer of synovial tissue	UBERON:0007616	43.55	gold quality
skeletal muscle tissue of rectus abdominis	UBERON:0004511	43.37	gold quality
substantia nigra pars compacta	UBERON:0001965	42.62	gold quality
secondary oocyte	CL:0000655	42.57	gold quality
muscle tissue	UBERON:0002385	42.51	gold quality
skeletal muscle tissue of biceps brachii	UBERON:0004502	42.18	gold quality
skeletal muscle tissue	UBERON:0001134	42.02	gold quality
biceps brachii	UBERON:0001507	41.97	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: no

miRNA regulators (miRDB)

14 targeting FAM47C, 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-3658	99.96	73.87	4379
HSA-MIR-3923	99.52	69.21	446
HSA-MIR-4452	99.50	68.45	1493
HSA-MIR-5683	99.36	68.59	2083
HSA-MIR-6852-5P	99.17	66.69	2073
HSA-MIR-628-3P	99.04	68.37	814
HSA-MIR-4712-3P	98.52	65.39	822
HSA-MIR-744-3P	97.99	67.76	637
HSA-MIR-4678	97.59	68.31	902
HSA-MIR-6501-5P	97.41	68.24	712
HSA-MIR-6509-5P	97.39	68.27	969
HSA-MIR-331-5P	96.59	67.94	705
HSA-MIR-345-5P	96.40	66.43	663
HSA-MIR-5681B	94.82	69.30	514

Cross-species orthologs

12 orthologs

Organism	Symbol	Gene ID
danio_rerio	fmn2b	ENSDARG00000061778
danio_rerio	fhdc2	ENSDARG00000099767
drosophila_melanogaster	capu	FBGN0000256
drosophila_melanogaster	dia	FBGN0011202
drosophila_melanogaster	form3	FBGN0053556
drosophila_melanogaster	Frl	FBGN0267795
caenorhabditis_elegans		WBGENE00000872
caenorhabditis_elegans	fhod-1	WBGENE00016735
caenorhabditis_elegans		WBGENE00018976
caenorhabditis_elegans		WBGENE00019030
caenorhabditis_elegans	sydn-1	WBGENE00021473
caenorhabditis_elegans		WBGENE00021698

Paralogs (18): DAAM1 (ENSG00000100592), FNBP4 (ENSG00000109920), DIAPH1 (ENSG00000131504), FHOD3 (ENSG00000134775), FHOD1 (ENSG00000135723), FHDC1 (ENSG00000137460), DIAPH3 (ENSG00000139734), DAAM2 (ENSG00000146122), DIAPH2 (ENSG00000147202), FMN2 (ENSG00000155816), FMNL2 (ENSG00000157827), FMNL3 (ENSG00000161791), FMNL1 (ENSG00000184922), FAM47A (ENSG00000185448), SHTN1 (ENSG00000187164), FAM47B (ENSG00000189132), INF2 (ENSG00000203485), GRID2IP (ENSG00000215045)

Protein

Protein identifiers

Putative protein FAM47C — Q5HY64 (reviewed: Q5HY64)

All UniProt accessions (1): Q5HY64

UniProt curated annotations — full annotation on UniProt →

Similarity. Belongs to the FAM47 family.

RefSeq proteins (1): NP_001013758* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR032743	FAM47	Family

Pfam: PF14642

UniProt features (13 total): compositionally biased region 7, region of interest 2, sequence conflict 2, chain 1, sequence variant 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q5HY64-F1	49.57	0.00

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 9 (showing top): ACEVEDO_LIVER_CANCER_WITH_H3K27ME3_UP, chrXp21, MIR3658, MIR628_3P, GSE15659_NAIVE_CD4_TCELL_VS_RESTING_TREG_UP, GSE15659_CD45RA_NEG_CD4_TCELL_VS_RESTING_TREG_UP, GSE26495_PD1HIGH_VS_PD1LOW_CD8_TCELL_DN, MCCABE_BOUND_BY_HOXC6, GSE46025_WT_VS_FOXO1_KO_KLRG1_LOW_CD8_EFFECTOR_TCELL_UP

GO Biological Process (0):

GO Molecular Function (0):

GO Cellular Component (0):

Protein interactions and networks

STRING

388 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
FAM47C	FAM186A	A6NE01	541
FAM47C	LRRC63	Q05C16	541
FAM47C	OR5F1	O95221	515
FAM47C	SPATA31A1	Q5TZJ5	507
FAM47C	TMEM128	Q5BJH2	506
FAM47C	ANKRD60	Q9BZ19	480
FAM47C	CCDC74B	Q96LY2	472
FAM47C	OR2T4	Q8NH00	450
FAM47C	KRTAP5-7	Q6L8G8	447
FAM47C	ZNF850	A8MQ14	446
FAM47C	C12orf42	Q96LP6	431
FAM47C	TTLL8	A6PVC2	419
FAM47C	CPXCR1	Q8N123	417
FAM47C	CCDC167	Q9P0B6	417
FAM47C	VCX3B	Q9H321	402

IntAct

0 interactions, top by confidence:

BioGRID (1): FAM47C (Affinity Capture-MS)

ESM2 similar proteins: A0A087WUL8, A0A0J9YWL9, A0A0J9YY54, A0A0U1RQI7, A6NJ88, A6QL64, B4DH59, D3ZVV1, E9Q6E9, F1LWT0, O04492, O88799, P0DKJ7, P0DKJ8, P0DKL2, P0DPF3, P18583, P53353, Q08AG5, Q0P6D6, Q2EG98, Q3BBV2, Q4ZJZ1, Q5HY64, Q5JPF3, Q5QGU6, Q5TAG4, Q5TI25, Q5XHX6, Q6P3W6, Q6P902, Q6XPR3, Q6ZQX7, Q86T75, Q86VE3, Q86VQ3, Q8N2N9, Q8N660, Q8N693, Q96EQ9

Diamond homologs: Q5HY64, Q5JRC9, Q6ZV65, Q8NA70, A6NHR8

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	1
Likely pathogenic	0
Uncertain significance	147
Likely benign	14
Benign	0

Top pathogenic / likely-pathogenic (1)

Variant ID	HGVS	Classification
816337	GRCh37/hg19 Xp21.1-11.3(chrX:32849282-43713387)x1	Pathogenic

SpliceAI

9 predictions. Top by Δscore:

Variant	Effect	Δscore
X:37008768:G:GT	donor_gain	0.7900
X:37008950:A:G	donor_gain	0.6500
X:37008944:T:A	donor_gain	0.3800
X:37008941:GCCTG:G	donor_gain	0.3200
X:37009061:TG:T	acceptor_gain	0.2600
X:37009062:GG:G	acceptor_gain	0.2600
X:37008610:A:G	donor_gain	0.2500
X:37009175:GTCC:G	donor_gain	0.2300
X:37008949:A:AG	donor_gain	0.2200

AlphaMissense

6676 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
X:37011363:T:C	F985L	0.978
X:37011365:C:A	F985L	0.978
X:37011365:C:G	F985L	0.978
X:37010981:G:C	W857C	0.967
X:37010981:G:T	W857C	0.967
X:37011426:T:A	W1006R	0.964
X:37011426:T:C	W1006R	0.964
X:37011354:T:C	F982L	0.961
X:37011356:T:A	F982L	0.961
X:37011356:T:G	F982L	0.961
X:37011411:T:C	F1001L	0.960
X:37011413:T:A	F1001L	0.960
X:37011413:T:G	F1001L	0.960
X:37011359:G:C	K983N	0.956
X:37011359:G:T	K983N	0.956
X:37011364:T:C	F985S	0.953
X:37010979:T:A	W857R	0.952
X:37010979:T:C	W857R	0.952
X:37011388:T:C	M993T	0.948
X:37011355:T:C	F982S	0.947
X:37011367:T:A	I986N	0.947
X:37010973:T:C	F855L	0.944
X:37010975:C:A	F855L	0.944
X:37010975:C:G	F855L	0.944
X:37011428:G:C	W1006C	0.943
X:37011428:G:T	W1006C	0.943
X:37008558:T:C	F50L	0.937
X:37008560:T:A	F50L	0.937
X:37008560:T:G	F50L	0.937
X:37011367:T:C	I986T	0.936

dbSNP variants (sampled 300 via entrez): RS112924019 (X:37008275 G>A,C), RS113171765 (X:37012123 G>A), RS113759376 (X:37009155 G>A,C), RS1157081154 (X:37011351 G>A,T), RS1158608468 (X:37007463 A>T), RS1158808820 (X:37009572 C>A,T), RS1160741979 (X:37008240 T>C), RS1160750367 (X:37006974 A>AT), RS1160786349 (X:37012068 G>C), RS1162216432 (X:37007780 C>G), RS1162401123 (X:37008401 G>A), RS1163528315 (X:37012161 A>G), RS1164468219 (X:37006980 G>C), RS1165492688 (X:37010036 C>G,T), RS1167932905 (X:37011742 A>G)

Disease associations

OMIM: gene MIM:301067 | disease phenotypes:

GenCC curated gene-disease

Disease	Classification	Inheritance
male infertility with azoospermia or oligozoospermia due to single gene mutation	Moderate	X-linked

Mondo (1): (MONDO:0018393)

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

2 total (human), top 2 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
Benzo(a)pyrene	affects methylation	1
Valproic Acid	increases methylation	1

Clinical trials (associated diseases)

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