FAM120A

family with sequence similarity 120A

Basic information

Region (hg38): 9:93451684-93566112

Previous symbols: [ "C9orf10" ]

Links

ENSG00000048828 ∙ NCBI:23196 ∙ OMIM:612265 ∙ HGNC:13247 ∙ Uniprot:Q9NZB2 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• Tourette syndrome (Limited), mode of inheritance: Unknown

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the FAM120A gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the FAM120A 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				2	3	5
missense			36	2		38
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding			5	2	24	31
Total	0	0	41	6	27

Variants in FAM120A

This is a list of pathogenic ClinVar variants found in the FAM120A region.

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

Position	Type	Phenotype	Significance	ClinVar
9-93452022-G-A		not specified	Uncertain significance (Apr 05, 2023)
9-93452028-G-A		not specified	Uncertain significance (Sep 14, 2022)
9-93452212-G-C		not specified	Uncertain significance (Mar 30, 2024)
9-93452218-G-T		not specified	Uncertain significance (May 31, 2023)
9-93452242-C-G		not specified	Uncertain significance (Mar 30, 2024)
9-93452248-G-C		not specified	Uncertain significance (Mar 30, 2024)
9-93452317-A-C		not specified	Likely benign (Mar 30, 2024)
9-93452405-C-T		not specified	Uncertain significance (Jan 19, 2022)
9-93452406-G-C		not specified	Uncertain significance (Jun 09, 2022)
9-93452439-CT-C			Likely benign (Dec 31, 2019)
9-93452516-C-T		not specified	Uncertain significance (Aug 04, 2023)
9-93452520-A-G		not specified	Uncertain significance (Jun 03, 2024)
9-93452547-T-C		not specified	Uncertain significance (Nov 27, 2023)
9-93452578-C-G		not specified	Uncertain significance (Oct 03, 2022)
9-93452581-A-G			Benign (Jul 14, 2018)
9-93452646-G-A			Benign (Jul 09, 2018)
9-93452690-A-G		not specified	Uncertain significance (May 16, 2024)
9-93471244-A-G		not specified	Uncertain significance (Mar 07, 2024)
9-93471408-A-T			Likely benign (Aug 01, 2022)
9-93476296-C-T			Benign (Jul 05, 2018)
9-93476449-C-T			Benign (Jul 09, 2018)
9-93497300-C-T			Benign (Jul 09, 2018)
9-93497538-G-A		not specified	Uncertain significance (Sep 23, 2023)
9-93497587-C-G		not specified	Uncertain significance (Oct 20, 2023)
9-93497601-T-TA			Benign (Oct 02, 2019)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
FAM120A	protein_coding	protein_coding	ENST00000277165	18	114394

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.00	0.00000459	125741	0	7	125748	0.0000278

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	3.35	410	650	0.630	0.0000377	7236
Missense in 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

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000199	0.000123
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000441	0.0000439
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

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

Haploinsufficiency Scores

• pHI: 0.249
• hipred: Y
• hipred_score: 0.673
• ghis: 0.636

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: K
• gene_indispensability_pred: N
• gene_indispensability_score: 0.156

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Fam120a

Gene ontology

• Cellular component: nucleus;cytosol;plasma membrane;membrane
• Molecular function: RNA binding