FAM186B

protein-coding

family with sequence similarity 186 member B

Gene summary

This gene product is a member of the FAM186 family, however, its exact function is not known. Alternatively spliced transcript variants have been found for this gene. [provided by RefSeq, Sep 2009]

Previous symbols:

C12orf25

MANE transcript

NM_032130.3

Inheritance

—

ClinVar variants

P:1U:137B:53

Top phenotype

Nephronophthisis

gnomAD constraint

pLI —, LoF o/e 0.94

Max pathogenic AF

—

Genomic locus

chr12:49,582,885-49,605,639

External References & Databases

Ensembl (ENSG00000135436)

Transcript & Mutation Effects

hg38 • Region Span ~22.8 kb

Loading mutation effect viewer...

GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to FAM186B variants in ClinVar

3 Conditions Cataloged

not specifiedTotal: 119

not providedTotal: 97

NephronophthisisTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_032130.3. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous			1 clinvar	13 clinvar	4 clinvar	18
missense			128 clinvar	22 clinvar	13 clinvar	163
nonsense			4 clinvar			4
start loss						0
frameshift			3 clinvar	1 clinvar		4
splice donor/acceptor (+/-2bp)		1 clinvar	1 clinvar			2
Total	0	1	137	36	17	191

Highest pathogenic variant AF is 0.00001874407

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 15 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_032130.3	RefSeq	NP_115506.1	7	MANE Select
ENST00000257894.2	Ensembl	ENSP00000257894.2	7	MANE Select
ENST00000532262.5	Ensembl	ENSP00000436995.1	4	Standard
ENST00000533372.1	Ensembl	ENSP00000433047.1	1	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Cellular Component

protein-containing complex

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000257894
Coding exons: 7
Length: 22755
Individuals with no LoFs: 125702
Homozygous LoFs: 0
Heterozygous LoFs: 46
Defined: 125748
p: 0.000183

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.796	449	499	0.900	0.0000274	5863
Missense (PolyPhen)		98	123.36	0.79442		1736
Synonymous	2.84	146	197	0.742	0.0000105	1724
Loss of Function	0.325	37	39.2	0.944	0.00000201	435

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00031	0.00031	rare
Latino/Admixed American	0	0.0	absent
Ashkenazi Jewish	0	0.0	absent
East Asian	0.0011	0.0011	notable
Finnish	0	0.0	absent
European (Non-Finnish)	0.00013	0.00012	rare
South Asian	0.00022	0.00020	rare
Other	0	0.0	absent

dbNSFP Gene Annotations

Source: dbNSFP

Intolerance Scores

LoFtool: 0.989
RVIS EVS: 1.41
RVIS percentile EVS: 94.8

Essentials

Essential (CRISPR): N
Essential (CRISPR2): S
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.0153

Gene Damage Prediction

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