FAM180A

family with sequence similarity 180 member A

Basic information

Region (hg38): 7:135728347-135748813

Links

ENSG00000189320 ∙ NCBI:389558 ∙ ∙ HGNC:33773 ∙ Uniprot:Q6UWF9 ∙ 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 FAM180A gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the FAM180A 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			10	1		11
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	10	1	0

Variants in FAM180A

This is a list of pathogenic ClinVar variants found in the FAM180A region.

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

Position	Type	Phenotype	Significance	ClinVar
7-135734003-C-T		not specified	Uncertain significance (Dec 20, 2023)
7-135734013-C-T		not specified	Uncertain significance (Jan 30, 2024)
7-135734030-A-G		not specified	Uncertain significance (Aug 17, 2022)
7-135734030-A-T		not specified	Uncertain significance (Dec 14, 2022)
7-135734090-C-A		not specified	Uncertain significance (Dec 19, 2022)
7-135734100-T-C		not specified	Likely benign (Sep 23, 2023)
7-135734136-C-T		not specified	Uncertain significance (Mar 20, 2024)
7-135734140-C-G		not specified	Uncertain significance (Jan 22, 2024)
7-135734160-T-C		not specified	Uncertain significance (Jul 13, 2021)
7-135737101-C-T		not specified	Uncertain significance (Jun 04, 2024)
7-135737130-G-A		not specified	Uncertain significance (Jan 02, 2024)
7-135737164-A-T		not specified	Uncertain significance (May 01, 2024)
7-135737175-C-T		not specified	Uncertain significance (Feb 16, 2023)
7-135748524-C-G		not specified	Uncertain significance (Jan 22, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
FAM180A	protein_coding	protein_coding	ENST00000338588	3	20499

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00100	0.609	125739	0	7	125746	0.0000278

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.200	110	104	1.06	0.00000649	1106
Missense in Polyphen		45	42.998	1.0466		452
Synonymous	0.510	44	48.5	0.907	0.00000314	368
Loss of Function	0.533	5	6.46	0.774	2.74e-7	80

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000154	0.000152
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000178	0.0000176
Middle Eastern	0.00	0.00
South Asian	0.0000327	0.0000327
Other	0.000164	0.000163

dbNSFP

Source: dbNSFP

Intolerance Scores

• loftool: 0.161
• rvis_EVS: -0.01
• rvis_percentile_EVS: 53.51

Haploinsufficiency Scores

• hipred: N
• hipred_score: 0.170
• ghis: 0.489

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.150

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Fam180a

Gene ontology

• Cellular component: extracellular region