FAM136A

family with sequence similarity 136 member A

Basic information

Region (hg38): 2:70295975-70302067

Links

ENSG00000035141 ∙ NCBI:84908 ∙ OMIM:616275 ∙ HGNC:25911 ∙ Uniprot:Q96C01 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• Meniere disease (Limited), mode of inheritance: Unknown

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the FAM136A gene.

• Meniere disease (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the FAM136A 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				3	1	4
missense			8	2	6	16
nonsense	1					1
start loss						0
frameshift				1		1
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region					1	1
non coding				1		1
Total	1	0	8	7	7

Variants in FAM136A

This is a list of pathogenic ClinVar variants found in the FAM136A region.

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

Position	Type	Phenotype	Significance	ClinVar
2-70297373-C-T		FAM136A-related disorder	Likely benign (Jul 30, 2019)
2-70297379-ACTGT-A			Likely benign (Aug 01, 2023)
2-70297444-C-G		FAM136A-related disorder	Benign (Mar 17, 2020)
2-70297445-G-A		FAM136A-related disorder	Benign (Jun 22, 2020)
2-70297473-C-T			Benign (Nov 01, 2022)
2-70300842-G-A		Meniere disease	Pathogenic (May 09, 2014)
2-70300866-C-A		FAM136A-related disorder • not specified	Conflicting classifications of pathogenicity (Oct 26, 2022)
2-70300913-T-C		not specified	Uncertain significance (Jan 29, 2024)
2-70300925-T-C		not specified	Uncertain significance (Jul 26, 2023)
2-70300928-A-G		not specified	Uncertain significance (Oct 02, 2023)
2-70300959-C-T		not specified	Uncertain significance (Sep 27, 2022)
2-70300967-C-T		not specified	Uncertain significance (Mar 20, 2024)
2-70301594-G-A		FAM136A-related disorder	Likely benign (Jan 22, 2020)
2-70301597-C-G		FAM136A-related disorder	Benign (Apr 12, 2019)
2-70301627-G-C		FAM136A-related disorder	Likely benign (May 20, 2019)
2-70301643-G-T		FAM136A-related disorder	Likely benign (Jun 14, 2019)
2-70301656-C-G		FAM136A-related disorder	Benign (Jul 30, 2019)
2-70301741-G-A		FAM136A-related disorder	Benign (Jul 12, 2019)
2-70301783-G-C			Likely benign (Jul 01, 2022)
2-70301851-G-A		FAM136A-related disorder	Benign (May 15, 2020)
2-70301905-T-G		FAM136A-related disorder	Benign (Jan 13, 2021)
2-70301940-G-A			Benign/Likely benign (Dec 01, 2022)
2-70301977-G-A		not specified	Uncertain significance (Feb 28, 2023)
2-70301982-C-G		not specified	Uncertain significance (Dec 16, 2023)
2-70301993-G-A		not specified	Uncertain significance (Apr 18, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
FAM136A	protein_coding	protein_coding	ENST00000037869	3	6116

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.000586	0.493	125695	0	53	125748	0.000211

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.0562	81	79.6	1.02	0.00000422	915
Missense in Polyphen		10	13.272	0.75345		206
Synonymous	0.149	25	26.0	0.963	0.00000119	234
Loss of Function	0.231	5	5.59	0.895	2.36e-7	68

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000387	0.000387
Ashkenazi Jewish	0.000104	0.0000992
East Asian	0.00	0.00
Finnish	0.000195	0.000185
European (Non-Finnish)	0.000344	0.000316
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Recessive Scores

• pRec: 0.109

Intolerance Scores

• loftool: 0.395
• rvis_EVS: -0.01
• rvis_percentile_EVS: 53.19

Haploinsufficiency Scores

• pHI: 0.235
• hipred: N
• hipred_score: 0.201
• ghis: 0.591

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.567

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Fam136a

Gene ontology

• Cellular component: cytoplasm