FAM120C

family with sequence similarity 120C

Basic information

Region (hg38): X:54068324-54183281

Previous symbols: [ "CXorf17" ]

Links

ENSG00000184083 ∙ NCBI:54954 ∙ OMIM:300741 ∙ HGNC:16949 ∙ Uniprot:Q9NX05 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the FAM120C gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the FAM120C gene is commonly pathogenic or not.

In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.

Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.

Variant type	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous				4	1	5
missense			29	1		30
nonsense			1			1
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region			1		1	2
non coding						0
Total	0	0	30	5	1

Variants in FAM120C

This is a list of pathogenic ClinVar variants found in the FAM120C region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
X-54073046-C-G		not specified	Uncertain significance (Dec 03, 2024)
X-54073047-G-A		not specified	Uncertain significance (Mar 06, 2025)
X-54073196-T-C		not specified	Uncertain significance (Aug 21, 2023)
X-54073221-C-T		not specified	Uncertain significance (Sep 25, 2024)
X-54073241-C-T		not specified	Uncertain significance (Aug 27, 2024)
X-54073244-C-T		not specified	Uncertain significance (Aug 02, 2021)
X-54081338-C-T		not specified	Uncertain significance (Feb 08, 2025)
X-54081347-C-T		not specified	Uncertain significance (Dec 28, 2023)
X-54081373-C-A		not specified	Uncertain significance (Dec 20, 2022)
X-54081388-C-T		not specified	Uncertain significance (Mar 02, 2023)
X-54081437-C-G		not specified	Uncertain significance (Jun 02, 2023)
X-54081450-T-C			Uncertain significance (Dec 17, 2020)
X-54085745-G-T		not specified	Uncertain significance (Feb 01, 2025)
X-54085827-C-T			Likely benign (Mar 01, 2023)
X-54085859-T-C		not specified	Uncertain significance (Feb 23, 2023)
X-54091307-C-A			Benign (Nov 11, 2019)
X-54116649-G-C		not specified	Uncertain significance (Oct 04, 2022)
X-54116701-G-A		not specified	Uncertain significance (May 22, 2023)
X-54116727-C-T			Likely benign (Sep 01, 2022)
X-54116764-G-A		not specified	Uncertain significance (Feb 16, 2023)
X-54132706-C-T		not specified	Uncertain significance (Mar 18, 2024)
X-54132719-C-T		not specified	Uncertain significance (Sep 14, 2023)
X-54132738-C-T			Likely benign (May 01, 2022)
X-54132771-T-C			Benign (Dec 04, 2018)
X-54133948-G-A			Uncertain significance (Oct 01, 2016)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
FAM120C	protein_coding	protein_coding	ENST00000375180	16	114958

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.00	0.0000208	124690	0	3	124693	0.0000120

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	3.63	200	406	0.492	0.0000301	7029
Missense in 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

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.000273	0.000199
East Asian	0.0000767	0.0000545
Finnish	0.00	0.00
European (Non-Finnish)	0.00	0.00
Middle Eastern	0.0000767	0.0000545
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Recessive Scores

• pRec: 0.103

Intolerance Scores

• loftool: 0.347
• rvis_EVS: -0.14
• rvis_percentile_EVS: 43.57

Haploinsufficiency Scores

• pHI: 0.532
• hipred: Y
• hipred_score: 0.572
• ghis: 0.532

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.205

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Fam120c
• Phenotype: normal phenotype

Gene ontology

• Cellular component: nucleus
• Molecular function: RNA binding