FAM149B1

family with sequence similarity 149 member B1

Basic information

Region (hg38): 10:73168119-73244504

Previous symbols: [ "KIAA0974" ]

Links

ENSG00000138286 ∙ NCBI:317662 ∙ OMIM:618413 ∙ HGNC:29162 ∙ Uniprot:Q96BN6 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• Joubert syndrome 36 (Limited), mode of inheritance: AR
• Joubert syndrome 36 (Strong), mode of inheritance: AR
• orofaciodigital syndrome type 6 (Supportive), mode of inheritance: AR
• Joubert syndrome 36 (Strong), mode of inheritance: AR
• Joubert syndrome 36 (Moderate), mode of inheritance: AR

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Joubert syndrome 36	AR	General	Genetic knowledge may be beneficial related to issues such as selection of optimal supportive care, informed medical decision-making, prognostic considerations, and avoidance of unnecessary testing	Craniofacial; Musculoskeletal; Neurologic; Ophthalmologic	30905400

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the FAM149B1 gene.

• not_specified (78 variants)
• not_provided (18 variants)
• Joubert_syndrome_36 (14 variants)
• FAM149B1-related_disorder (3 variants)
• Joubert_syndrome (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the FAM149B1 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000173348.2. Only rare variants are included in the table.

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.

Effect	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous			2	9		11
missense			76	5		81
nonsense	2	3	1			6
start loss			1			1
frameshift	1	2	4			7
splice donor/acceptor (+/-2bp)	1	1	2			4
Total	4	6	86	14	0

Highest pathogenic variant AF is 0.00003737118

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
FAM149B1	protein_coding	protein_coding	ENST00000242505	14	76339

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
2.49e-13	0.407	0	0	0	0	0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.56	223	299	0.746	0.0000154	3762
Missense in Polyphen		71	97.535	0.72795		1255
Synonymous	0.937	100	113	0.888	0.00000632	1145
Loss of Function	1.34	24	32.2	0.746	0.00000199	382

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)	0.00	0.00
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Intolerance Scores

• rvis_EVS: 0.73
• rvis_percentile_EVS: 85.98

Haploinsufficiency Scores

• pHI: 0.674
• ghis: 0.403

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.00767

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Fam149b