FAM120A

protein-coding

family with sequence similarity 120A

Gene summary

Enables RNA binding activity. Located in cytosol. [provided by Alliance of Genome Resources, Jul 2025]

Previous symbols:

C9orf10

MANE transcript

NM_014612.5

Inheritance

—

ClinVar variants

U:123B:9

Top phenotype

Neurodevelopmental disorder

gnomAD constraint

pLI —, LoF o/e 0.06

Max pathogenic AF

—

Genomic locus

chr9:93,451,685-93,566,112

External References & Databases

Ensembl (ENSG00000048828)

Transcript & Mutation Effects

hg38 • Region Span ~114.4 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

Tourette syndromeLIMITED

Inheritance Pattern: Unknown

Disease ID:MONDO:0007661

Submitter: Labcorp Genetics (formerly Invitae)

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to FAM120A variants in ClinVar

3 Conditions Cataloged

not specifiedTotal: 135

not providedTotal: 12

Neurodevelopmental disorderTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_014612.5. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous			4 clinvar	4 clinvar		8
missense			112 clinvar	5 clinvar		117
nonsense						0
start loss						0
frameshift			2 clinvar			2
splice donor/acceptor (+/-2bp)			5 clinvar			5
Total	0	0	123	9	0	132

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 33 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_014612.5	RefSeq	NP_055427.2	18	MANE Select
ENST00000277165.11	Ensembl	ENSP00000277165.5	18	MANE Select
NM_001286722.2	RefSeq	NP_001273651.1	18	Standard
NM_001286723.2	RefSeq	NP_001273652.1	10	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Molecular Function

RNA binding

Cellular Component

nucleus
cytosol
plasma membrane
membrane

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000277165
Coding exons: 18
Length: 114394
Individuals with no LoFs: 125741
Homozygous LoFs: 0
Heterozygous LoFs: 7
Defined: 125748
p: 0.0000278

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	3.35	410	650	0.630	0.0000377	7236
Missense (PolyPhen)		103	225.92	0.45591		2500
Synonymous	0.748	252	268	0.942	0.0000173	2270
Loss of Function	5.99	3	47.6	0.0630	0.00000228	569

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00020	0.00012	rare
Latino/Admixed American	0	0.0	absent
Ashkenazi Jewish	0	0.0	absent
East Asian	0	0.0	absent
Finnish	0	0.0	absent
European (Non-Finnish)	0.000044	0.000044	rare
South Asian	0	0.0	absent
Other	0	0.0	absent

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: May participate in mRNA transport in the cytoplasm (By similarity). Critical component of the oxidative stress-induced survival signaling. Activates src family kinases and acts as a scaffolding protein enabling src family kinases to phosphorylate and activate PI3-kinase. Binds RNA and promotes the secretion of IGF-II. May play a pivotal role in the progression of scirrhous- type gastric cancer by supporting cancer cell survival in environments with various oxidative stresses. {ECO:0000250, ECO:0000269|PubMed:19015244}.;

Recessive Scores

pRec: 0.110

Intolerance Scores

LoFtool: 0.393
RVIS EVS: -2.04
RVIS percentile EVS: 1.66

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): K
Indispensability pred.: N
Indispensability score: 0.156

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium