FAM98C

Summary

FAM98C (family with sequence similarity 98 member C, HGNC:27119) is a protein-coding gene on chromosome 19q13.2, encoding Protein FAM98C (Q17RN3).

Predicted to be part of tRNA-splicing ligase complex.

Source: NCBI Gene 147965 — RefSeq curated summary.

At a glance

• Clinical variants (ClinVar): 92 total — 1 likely-pathogenic
• MANE Select transcript: NM_174905

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:27119
Approved symbol	FAM98C
Name	family with sequence similarity 98 member C
Location	19q13.2
Locus type	gene with protein product
Status	Approved
Aliases	FLJ44669
Ensembl gene	ENSG00000130244
Ensembl biotype	protein_coding
Entrez	147965

Gene structure

Transcript identifiers

Ensembl transcripts: 16 — 10 protein_coding, 4 retained_intron, 1 protein_coding_CDS_not_defined, 1 nonsense_mediated_decay

ENST00000252530, ENST00000343358, ENST00000585954, ENST00000586372, ENST00000588262, ENST00000588348, ENST00000589027, ENST00000589029, ENST00000589408, ENST00000592992, ENST00000909362, ENST00000909363, ENST00000909364, ENST00000909365, ENST00000909366, ENST00000909367

RefSeq mRNA: 2 — MANE Select: NM_174905 NM_001351675, NM_174905

CCDS: CCDS42562, CCDS86763

Canonical transcript exons

ENST00000252530 — 8 exons

Exon	Start	End
ENSE00001144295	38405519	38405635
ENSE00002816138	38408751	38409084
ENSE00003511783	38403560	38403694
ENSE00003559014	38405344	38405421
ENSE00003559719	38404908	38405113
ENSE00003620121	38406910	38407077
ENSE00003684392	38403338	38403486
ENSE00003923147	38403093	38403218

Expression profiles

Bgee: expression breadth ubiquitous, 239 present calls, max score 93.03.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 7.6562 / max 74.3740, expressed in 1737 samples.

FANTOM5 promoters (2 alternative TSS)

Promoter ID	TPM avg	Samples expressed
175631	5.5624	1638
175632	2.0938	968

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
right hemisphere of cerebellum	UBERON:0014890	93.03	gold quality
cerebellar cortex	UBERON:0002129	92.70	gold quality
cerebellar hemisphere	UBERON:0002245	92.70	gold quality
cerebellum	UBERON:0002037	92.11	gold quality
cerebellar vermis	UBERON:0004720	91.90	gold quality
prefrontal cortex	UBERON:0000451	91.52	gold quality
upper arm skin	UBERON:0004263	91.47	gold quality
right frontal lobe	UBERON:0002810	90.95	gold quality
anterior cingulate cortex	UBERON:0009835	90.87	gold quality
Brodmann (1909) area 9	UBERON:0013540	90.83	gold quality
ileal mucosa	UBERON:0000331	90.79	gold quality
mucosa of transverse colon	UBERON:0004991	90.69	gold quality
granulocyte	CL:0000094	90.52	gold quality
amygdala	UBERON:0001876	89.61	gold quality
frontal cortex	UBERON:0001870	89.54	gold quality
putamen	UBERON:0001874	89.52	gold quality
skin of abdomen	UBERON:0001416	89.47	gold quality
dorsolateral prefrontal cortex	UBERON:0009834	89.47	gold quality
nucleus accumbens	UBERON:0001882	89.43	gold quality
neocortex	UBERON:0001950	89.21	gold quality
skin of leg	UBERON:0001511	89.16	gold quality
C1 segment of cervical spinal cord	UBERON:0006469	88.80	gold quality
hypothalamus	UBERON:0001898	88.42	gold quality
zone of skin	UBERON:0000014	88.36	gold quality
caudate nucleus	UBERON:0001873	88.29	gold quality
spinal cord	UBERON:0002240	88.02	gold quality
apex of heart	UBERON:0002098	88.01	gold quality
cerebral cortex	UBERON:0000956	87.88	gold quality
brain	UBERON:0000955	87.84	gold quality
right uterine tube	UBERON:0001302	87.78	gold quality

Single-cell (SCXA)

Detected in 2 experiment(s), a significant marker in 1.

Experiment	Marker?	Max mean expression
E-ANND-3	yes	4.40
E-MTAB-7606	no	222.46

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

15 targeting FAM98C, 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-6132	99.60	65.83	1554
HSA-MIR-6836-5P	99.60	65.62	1538
HSA-MIR-513A-3P	99.39	70.63	3620
HSA-MIR-513C-3P	99.39	70.63	3620
HSA-MIR-3191-5P	99.24	66.52	1722
HSA-MIR-3606-3P	99.11	69.84	3254
HSA-MIR-328-5P	99.08	64.65	1000
HSA-MIR-6885-5P	98.71	64.33	902
HSA-MIR-518C-5P	98.53	69.20	1640
HSA-MIR-6810-5P	98.29	66.21	975
HSA-MIR-450A-2-3P	97.91	67.56	1459
HSA-MIR-3664-3P	97.85	67.62	1452
HSA-MIR-215-3P	97.02	68.01	1209
HSA-MIR-4652-5P	96.46	64.22	553
HSA-MIR-5681B	94.82	69.30	514

Cross-species orthologs

5 orthologs

Organism	Symbol	Gene ID
danio_rerio	fam98a	ENSDARG00000078391
mus_musculus	Fam98c	ENSMUSG00000030590
rattus_norvegicus	Fam98c	ENSRNOG00000024036
drosophila_melanogaster	CG5913	FBGN0039385
caenorhabditis_elegans		WBGENE00044326

Paralogs (2): FAM98A (ENSG00000119812), FAM98B (ENSG00000171262)

Protein

Protein identifiers

Protein FAM98C — Q17RN3 (reviewed: Q17RN3)

All UniProt accessions (4): Q17RN3, K7EQL1, K7EQT7, K7ES49

UniProt curated annotations — full annotation on UniProt →

Similarity. Belongs to the FAM98 family.

Isoforms (2)

UniProt ID	Names	Canonical?
Q17RN3-1	1	yes
Q17RN3-2	2

RefSeq proteins (2): NP_001338604, NP_777565* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR018797	FAM98	Family

Pfam: PF10239

UniProt features (5 total): splice variant 2, chain 1, region of interest 1, sequence variant 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q17RN3-F1	79.51	0.27

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 83 (showing top): GOCC_TRNA_SPLICING_LIGASE_COMPLEX, GSE13522_CTRL_VS_T_CRUZI_Y_STRAIN_INF_SKIN_129_MOUSE_DN, CEBPZ_TARGET_GENES, GLI3_TARGET_GENES, ID2_TARGET_GENES, NAB2_TARGET_GENES, RYBP_TARGET_GENES, TERF1_TARGET_GENES, ZNF10_TARGET_GENES, ZNF257_TARGET_GENES, ZNF391_TARGET_GENES, ZSCAN31_TARGET_GENES, MIR3664_3P, MIR215_3P, MIR328_5P

GO Biological Process (0):

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

GO Cellular Component (1): tRNA-splicing ligase complex (GO:0072669)

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
binding	1
intracellular protein-containing complex	1
catalytic complex	1

Protein interactions and networks

STRING

344 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
FAM98C	YIPF6	Q96EC8	509
FAM98C	TXNDC15	Q96J42	493
FAM98C	RNPEPL1	Q9HAU8	493
FAM98C	METTL26	Q96S19	480
FAM98C	LRRCC1	Q9C099	479
FAM98C	FAM133B	Q5BKY9	476
FAM98C	ZNF559	Q9BR84	473
FAM98C	CEP41	Q9BYV8	451
FAM98C	TMEM256	Q8N2U0	433
FAM98C	ABHD8	Q96I13	414
FAM98C	CD2BP2	O95400	413
FAM98C	CAPN12	Q6ZSI9	400
FAM98C	SACK1F	Q8NEG4	394
FAM98C	INTS13	Q9NVM9	394
FAM98C	CORO7	P57737	380
FAM98C	NOL3	O60936	380

IntAct

48 interactions, top by confidence:

A	B	Type	Score
FAM98C	DMWD	psi-mi:“MI:0915”(physical association)	0.560
DR1	FAM98C	psi-mi:“MI:0915”(physical association)	0.560
GRN	FAM98C	psi-mi:“MI:0915”(physical association)	0.560
GTF2B	FAM98C	psi-mi:“MI:0915”(physical association)	0.560
FAM98C	HSPB1	psi-mi:“MI:0915”(physical association)	0.560
TSC1	FAM98C	psi-mi:“MI:0915”(physical association)	0.560
FAM98C	WFS1	psi-mi:“MI:0915”(physical association)	0.560
FAM98C	GTF3C3	psi-mi:“MI:0915”(physical association)	0.560
FAM98C	KIF1B	psi-mi:“MI:0915”(physical association)	0.560
FAM98C	RNF11	psi-mi:“MI:0915”(physical association)	0.560
FAM98C	SPRED1	psi-mi:“MI:0915”(physical association)	0.560
TARDBP	FAM98C	psi-mi:“MI:0915”(physical association)	0.560

BioGRID (8): FAM98C (Affinity Capture-MS), FAM98C (Proximity Label-MS), FAM98C (Affinity Capture-MS), FAM98C (Affinity Capture-MS), FAM98C (Affinity Capture-MS), FAM98C (Proximity Label-MS), C14orf166 (Cross-Linking-MS (XL-MS)), FAM98C (Proximity Label-MS)

ESM2 similar proteins: A4GXA9, A7E3N7, A8VU90, D3KCC4, D3ZZN9, G3V8H4, O08672, O95382, Q13608, Q13671, Q14296, Q17RN3, Q28616, Q3UR50, Q3UR97, Q3V3V9, Q4KM32, Q53GL7, Q56A04, Q58CQ5, Q58EX7, Q5BK61, Q5NVA9, Q62893, Q643R3, Q66H85, Q6F5E8, Q6NVH7, Q6ZW31, Q7T0L4, Q80UU1, Q80XL1, Q8BJW7, Q8BTN6, Q8CIE4, Q8CJ00, Q8K592, Q8N2G8, Q8NAG6, Q8VCI7

Diamond homologs: Q17RN3, Q3TJZ6, Q52LJ0, Q5FWT1, Q5R679, Q80VD1, Q8NCA5

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	1
Uncertain significance	64
Likely benign	12
Benign	6

Top pathogenic / likely-pathogenic (1)

Variant ID	HGVS	Classification
266079	NM_174905.4(FAM98C):c.844C>T (p.Arg282Ter)	Likely pathogenic

SpliceAI

1179 predictions. Top by Δscore:

Variant	Effect	Δscore
19:38403690:GCTGC:G	donor_gain	1.0000
19:38403693:GC:G	donor_gain	1.0000
19:38403695:G:GG	donor_gain	1.0000
19:38405619:G:GT	donor_gain	1.0000
19:38403172:G:GT	donor_gain	0.9900
19:38403465:G:GT	donor_gain	0.9900
19:38403554:TCGCA:T	acceptor_loss	0.9900
19:38403557:CA:C	acceptor_loss	0.9900
19:38403558:A:AG	acceptor_gain	0.9900
19:38403558:A:AT	acceptor_loss	0.9900
19:38403559:G:GA	acceptor_gain	0.9900
19:38403559:G:T	acceptor_loss	0.9900
19:38403691:C:G	donor_gain	0.9900
19:38403691:CTGC:C	donor_gain	0.9900
19:38403692:TGC:T	donor_gain	0.9900
19:38403692:TGCGT:T	donor_loss	0.9900
19:38403693:GCG:G	donor_gain	0.9900
19:38403694:CG:C	donor_loss	0.9900
19:38403695:G:GC	donor_loss	0.9900
19:38403696:T:A	donor_loss	0.9900
19:38403697:GAGTC:G	donor_loss	0.9900
19:38403698:AG:A	donor_loss	0.9900
19:38403699:G:C	donor_loss	0.9900
19:38403706:G:GT	donor_gain	0.9900
19:38405109:C:G	donor_gain	0.9900
19:38406903:A:AG	acceptor_gain	0.9900
19:38406904:C:G	acceptor_gain	0.9900
19:38406907:CAG:C	acceptor_loss	0.9900
19:38406908:A:AG	acceptor_gain	0.9900
19:38406909:G:GC	acceptor_gain	0.9900

AlphaMissense

2189 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
19:38405612:T:C	F243L	0.974
19:38405614:C:A	F243L	0.974
19:38405614:C:G	F243L	0.974
19:38404910:T:C	F118L	0.967
19:38404912:T:A	F118L	0.967
19:38404912:T:G	F118L	0.967
19:38405613:T:C	F243S	0.941
19:38405598:T:C	L238P	0.937
19:38408784:C:A	R318S	0.936
19:38405567:C:A	R228S	0.935
19:38405592:T:C	L236P	0.929
19:38407001:C:A	A281D	0.929
19:38408819:G:C	W329C	0.923
19:38408819:G:T	W329C	0.923
19:38405571:G:C	R229P	0.921
19:38404911:T:C	F118S	0.920
19:38405588:C:A	R235S	0.917
19:38408817:T:A	W329R	0.917
19:38408817:T:C	W329R	0.917
19:38405568:G:C	R228P	0.916
19:38407000:G:C	A281P	0.912
19:38403580:T:C	F79L	0.905
19:38403582:T:A	F79L	0.905
19:38403582:T:G	F79L	0.905
19:38405589:G:C	R235P	0.903
19:38408774:C:A	D314E	0.903
19:38408774:C:G	D314E	0.903
19:38408767:T:A	V312D	0.899
19:38408776:G:C	R315P	0.894
19:38404924:G:C	E122D	0.891

dbSNP variants (sampled 300 via entrez): RS1000440222 (19:38405758 T>C), RS1000955356 (19:38401965 G>A), RS1001446188 (19:38406934 G>A), RS1001990772 (19:38402903 A>G), RS1002148694 (19:38405859 ATTTTT>A,AT,ATT,ATTT,ATTTT,ATTTTTT,ATTTTTTT,ATTTTTTTT,ATTTTTTTTT,ATTTTTTTTTT,ATTTTTTTTTTT), RS1002692214 (19:38404072 A>G), RS1002985618 (19:38404046 G>A), RS1003192888 (19:38408700 C>G), RS1003700809 (19:38402967 G>GGGGCGGGGC), RS1004036821 (19:38406570 G>A), RS1004063984 (19:38402877 G>A), RS1004841896 (19:38408197 G>A,T), RS1004929020 (19:38403711 A>G), RS1005437662 (19:38409211 T>A), RS1005599389 (19:38409287 C>G)

Disease associations

OMIM: gene `` | disease phenotypes: MIM:613091

GenCC curated gene-disease

Mondo (2): autism spectrum disorder (MONDO:0005258), asphyxiating thoracic dystrophy 3 (MONDO:0013127)

Orphanet (5): Jeune syndrome (Orphanet:474), Short rib-polydactyly syndrome, Majewski type (Orphanet:93269), Short rib-polydactyly syndrome, Saldino-Noonan type (Orphanet:93270), Short rib-polydactyly syndrome, Verma-Naumoff type (Orphanet:93271), NON RARE IN EUROPE: Autism (Orphanet:106)

HPO phenotypes

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

GWAS associations

0 associations (top):

MeSH disease descriptors (1)

Descriptor	Name	Tree numbers
C537602	Short rib-polydactyly syndrome, Verma-Naumoff type (supp.)

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

27 total (human), top 27 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
Aflatoxin B1	increases expression	2
bisphenol F	affects cotreatment, increases expression	1
bufotalin	decreases expression	1
triphenyl phosphate	affects expression	1
bisphenol A	increases expression	1
lead acetate	increases expression	1
CGP 52608	increases reaction, affects binding	1
perfluoro-n-nonanoic acid	increases expression	1
monomethylarsonous acid	decreases expression	1
nutlin 3	affects cotreatment, increases expression	1
jinfukang	affects cotreatment, increases expression	1
(+)-JQ1 compound	decreases expression	1
Sunitinib	decreases expression	1
Acetaminophen	decreases expression	1
Camptothecin	increases expression	1
Cisplatin	affects cotreatment, increases expression	1
Dactinomycin	affects cotreatment, increases expression	1
Dexamethasone	affects cotreatment, increases expression	1
Ethyl Methanesulfonate	increases expression	1
Formaldehyde	increases expression	1
Indomethacin	increases expression, affects cotreatment	1
Lead	affects expression	1
Methyl Methanesulfonate	increases expression	1
Smoke	decreases expression	1
1-Methyl-3-isobutylxanthine	affects cotreatment, increases expression	1
Sodium Selenite	increases expression	1
Copper Sulfate	increases expression	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