FAM178B

family with sequence similarity 178 member B

Basic information

Region (hg38): 2:96875881-96986580

Links

ENSG00000168754 ∙ NCBI:51252 ∙ ∙ HGNC:28036 ∙ Uniprot:Q8IXR5 ∙ 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 FAM178B gene.

• Inborn genetic diseases (15 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the FAM178B 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			11	3		14
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	12	3	0

Variants in FAM178B

This is a list of pathogenic ClinVar variants found in the FAM178B region.

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

Position	Type	Phenotype	Significance	ClinVar
2-96877946-G-T		not specified	Uncertain significance (Jan 04, 2022)
2-96877963-C-T		not specified	Likely benign (May 31, 2022)
2-96877988-G-A		not specified	Uncertain significance (Jun 22, 2023)
2-96878462-A-C		not specified	Uncertain significance (Apr 07, 2022)
2-96878492-G-A		not specified	Likely benign (Dec 01, 2022)
2-96894008-G-C		not specified	Uncertain significance (May 09, 2023)
2-96894036-G-A		not specified	Uncertain significance (Jul 12, 2022)
2-96894036-G-C		not specified	Uncertain significance (Jan 31, 2024)
2-96894044-G-A		not specified	Likely benign (Dec 31, 2023)
2-96970765-C-A		not specified	Uncertain significance (Jul 14, 2021)
2-96971977-G-C		not specified	Uncertain significance (Jun 22, 2021)
2-96972052-A-C		not specified	Uncertain significance (Jun 18, 2021)
2-96972055-A-C		not specified	Uncertain significance (Jun 18, 2021)
2-96972061-A-C		not specified	Uncertain significance (Aug 12, 2021)
2-96972133-C-T		not specified	Uncertain significance (Jul 28, 2021)
2-96972149-A-G		not specified	Uncertain significance (Aug 02, 2021)
2-96972302-C-T		not specified	Likely benign (Oct 26, 2021)
2-96972555-G-A		not specified	Uncertain significance (Aug 30, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
FAM178B	protein_coding	protein_coding	ENST00000490605	17	142556

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
8.21e-13	0.865	125517	0	27	125544	0.000108

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.01	300	353	0.849	0.0000194	4343
Missense in Polyphen		68	85.051	0.79952		1157
Synonymous	1.97	121	152	0.797	0.00000842	1367
Loss of Function	1.93	25	37.8	0.662	0.00000177	408

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000310	0.000308
Ashkenazi Jewish	0.000100	0.0000993
East Asian	0.000163	0.000163
Finnish	0.00	0.00
European (Non-Finnish)	0.0000178	0.0000176
Middle Eastern	0.000163	0.000163
South Asian	0.000528	0.000523
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Intolerance Scores

• loftool: 0.926
• rvis_EVS: 0.84
• rvis_percentile_EVS: 88.3

Haploinsufficiency Scores

• hipred: N
• hipred_score: 0.123
• ghis: 0.428

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.670

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Fam178b