FAM78B

family with sequence similarity 78 member B, the group of MicroRNA protein coding host genes

Basic information

Region (hg38): 1:166057426-166167001

Links

ENSG00000188859 ∙ NCBI:149297 ∙ ∙ HGNC:13495 ∙ Uniprot:Q5VT40 ∙ 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 FAM78B gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the FAM78B 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			14			14
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	14	0	0

Variants in FAM78B

This is a list of pathogenic ClinVar variants found in the FAM78B region.

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

Position	Type	Phenotype	Significance	ClinVar
1-166070266-G-T		not specified	Uncertain significance (Dec 23, 2024)
1-166070275-C-T		not specified	Uncertain significance (Oct 12, 2021)
1-166070289-C-T		not specified	Uncertain significance (Jul 17, 2023)
1-166070348-C-T		not specified	Uncertain significance (Oct 09, 2024)
1-166070353-C-T		not specified	Uncertain significance (Dec 06, 2022)
1-166070357-T-C		not specified	Uncertain significance (May 02, 2024)
1-166070365-C-T		not specified	Uncertain significance (Oct 20, 2021)
1-166070399-G-A		not specified	Uncertain significance (Dec 03, 2024)
1-166070457-C-A		not specified	Uncertain significance (Apr 08, 2024)
1-166070462-T-C		not specified	Uncertain significance (Oct 12, 2021)
1-166070491-G-A		not specified	Uncertain significance (May 23, 2023)
1-166070560-T-C		not specified	Uncertain significance (Dec 09, 2023)
1-166070618-T-C		not specified	Uncertain significance (Dec 11, 2024)
1-166070653-A-G		not specified	Uncertain significance (Jul 28, 2021)
1-166070659-G-A		not specified	Uncertain significance (Nov 08, 2024)
1-166166055-G-A		not specified	Uncertain significance (Mar 15, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
FAM78B	protein_coding	protein_coding	ENST00000338353	2	109533

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.311	0.673	125736	0	4	125740	0.0000159

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.55	100	154	0.649	0.00000778	1711
Missense in Polyphen		25	56.341	0.44372		652
Synonymous	0.322	56	59.2	0.947	0.00000283	525
Loss of Function	2.03	2	8.31	0.241	3.56e-7	88

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000292	0.0000292
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000268	0.0000264
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Intolerance Scores

• rvis_EVS: -0.36
• rvis_percentile_EVS: 28.63

Haploinsufficiency Scores

• pHI: 0.765
• hipred: Y
• hipred_score: 0.736
• ghis: 0.657

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.303

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Fam78b