FAM120C

protein-coding

family with sequence similarity 120C

Gene summary

This gene encodes a potential transmembrane protein and lies in a region where mutations and deletions have been associated with intellectual disability and autism. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Aug 2011]

Previous symbols:

CXorf17

MANE transcript

NM_017848.6

Inheritance

—

ClinVar variants

U:173B:6

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.03

Max pathogenic AF

—

Genomic locus

chrX:54,068,324-54,183,281

External References & Databases

Ensembl (ENSG00000184083)

Transcript & Mutation Effects

hg38 • Region Span ~115.0 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to FAM120C variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 57

not providedTotal: 9

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_017848.6. 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			26 clinvar	4 clinvar	1 clinvar	31
missense			113 clinvar	1 clinvar		114
nonsense			11 clinvar			11
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			23 clinvar			23
Total	0	0	173	5	1	179

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 12 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_017848.6	RefSeq	NP_060318.4	16	MANE Select
ENST00000375180.7	Ensembl	ENSP00000364324.2	16	MANE Select
NM_001300788.2	RefSeq	NP_001287717.1	14	Standard
NM_198456.3	RefSeq	NP_940858.2	2	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Molecular Function

RNA binding

Cellular Component

nucleus

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000375180
Coding exons: 16
Length: 114958
Individuals with no LoFs: 124690
Homozygous LoFs: 0
Heterozygous LoFs: 3
Defined: 124693
p: 0.0000120

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	3.63	200	406	0.492	0.0000301	7029
Missense (PolyPhen)		43	148.63	0.28932		2664
Synonymous	0.160	156	159	0.984	0.0000112	2299
Loss of Function	5.31	1	34.8	0.0287	0.00000296	516

Population LoF Frequency

Population	CAF	p-value	Status
African	0	0.0	absent
Latino/Admixed American	0	0.0	absent
Ashkenazi Jewish	0.00027	0.00020	rare
East Asian	0.000077	0.000055	rare
Finnish	0	0.0	absent
European (Non-Finnish)	0	0.0	absent
South Asian	0	0.0	absent
Other	0	0.0	absent

dbNSFP Gene Annotations

Source: dbNSFP

Recessive Scores

pRec: 0.103

Intolerance Scores

LoFtool: 0.347
RVIS EVS: -0.14
RVIS percentile EVS: 43.57

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.205

Gene Damage Prediction

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