FAM120A2P

family with sequence similarity 120A2, pseudogene

Basic information

Region (hg38): 9:93335374-93346152

Previous symbols: [ "C9orf129" ]

Links

ENSG00000204352 ∙ NCBI:445577 ∙ ∙ HGNC:31116 ∙ Uniprot:Q5T035 ∙ 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 FAM120A2P gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the FAM120A2P 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						0
missense						0
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding				1		1
Total	0	0	0	1	0

Variants in FAM120A2P

This is a list of pathogenic ClinVar variants found in the FAM120A2P region.

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

Position	Type	Phenotype	Significance	ClinVar
9-93335406-G-A			Likely benign (Sep 01, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
FAM120A2P	protein_coding	protein_coding	ENST00000375419	4	28216

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.000298	0.364	125716	0	26	125742	0.000103

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.206	104	110	0.945	0.00000702	1248
Missense in Polyphen		10	10.986	0.91024		120
Synonymous	-0.620	57	51.4	1.11	0.00000400	408
Loss of Function	-0.174	5	4.60	1.09	1.94e-7	67

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000393	0.000333
Ashkenazi Jewish	0.00	0.00
East Asian	0.000169	0.000163
Finnish	0.00	0.00
European (Non-Finnish)	0.000153	0.000132
Middle Eastern	0.000169	0.000163
South Asian	0.00	0.00
Other	0.000179	0.000163

dbNSFP

Source: dbNSFP

Intolerance Scores

• loftool: 0.800
• rvis_EVS: 0.66
• rvis_percentile_EVS: 84.35

Haploinsufficiency Scores

• hipred: N
• hipred_score: 0.329
• ghis: 0.448

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N

Gene Damage Prediction

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

Gene ontology

• Cellular component: nucleus