FAM78A

family with sequence similarity 78 member A

Basic information

Region (hg38): 9:131258076-131277365

Previous symbols: [ "C9orf59" ]

Links

ENSG00000126882 ∙ NCBI:286336 ∙ ∙ HGNC:25465 ∙ Uniprot:Q5JUQ0 ∙ 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 FAM78A gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the FAM78A 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			32			32
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	32	0	0

Variants in FAM78A

This is a list of pathogenic ClinVar variants found in the FAM78A region.

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

Position	Type	Phenotype	Significance	ClinVar
9-131260838-G-A		not specified	Uncertain significance (Dec 13, 2024)
9-131260872-G-A		not specified	Uncertain significance (Feb 13, 2023)
9-131260917-C-T		not specified	Uncertain significance (Oct 12, 2021)
9-131260979-C-T		not specified	Uncertain significance (Dec 19, 2022)
9-131260989-C-T		not specified	Uncertain significance (Dec 12, 2022)
9-131261006-C-T		not specified	Uncertain significance (Oct 29, 2024)
9-131261007-G-A		not specified	Uncertain significance (Dec 21, 2023)
9-131261012-G-A		not specified	Uncertain significance (Jul 25, 2023)
9-131261070-C-T		not specified	Uncertain significance (Jun 16, 2024)
9-131261094-C-T		not specified	Uncertain significance (Jun 28, 2024)
9-131261121-G-A		not specified	Uncertain significance (Jul 26, 2024)
9-131261166-C-T		not specified	Uncertain significance (Jun 10, 2024)
9-131261178-C-T		not specified	Uncertain significance (Feb 10, 2022)
9-131261189-A-G		not specified	Uncertain significance (Aug 05, 2024)
9-131261241-C-T		not specified	Uncertain significance (Jun 05, 2024)
9-131261268-C-T		not specified	Uncertain significance (Dec 01, 2022)
9-131261298-C-T		not specified	Uncertain significance (Aug 05, 2024)
9-131261322-C-G		not specified	Uncertain significance (Dec 21, 2023)
9-131261323-C-A		not specified	Uncertain significance (Jul 09, 2021)
9-131261331-C-T		not specified	Uncertain significance (Jan 16, 2024)
9-131275939-G-T		not specified	Uncertain significance (Oct 24, 2024)
9-131275942-T-C		not specified	Uncertain significance (May 15, 2024)
9-131275957-C-T		not specified	Uncertain significance (Aug 26, 2024)
9-131276004-C-A		not specified	Uncertain significance (Mar 08, 2024)
9-131276047-C-T		not specified	Uncertain significance (Jun 09, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
FAM78A	protein_coding	protein_coding	ENST00000372271	2	18472

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.373	0.617	125700	0	13	125713	0.0000517

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.80	124	195	0.636	0.0000130	1870
Missense in Polyphen		50	98.019	0.5101		866
Synonymous	0.223	80	82.6	0.969	0.00000613	553
Loss of Function	2.17	2	9.02	0.222	3.89e-7	89

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000444	0.0000440
Middle Eastern	0.00	0.00
South Asian	0.000262	0.000261
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Recessive Scores

• pRec: 0.122

Intolerance Scores

• loftool: 0.230
• rvis_EVS: -0.43
• rvis_percentile_EVS: 25.15

Haploinsufficiency Scores

• pHI: 0.231
• hipred: Y
• hipred_score: 0.665
• ghis: 0.583

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.998

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Fam78a