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

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.

• Joubert syndrome 36 (2 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.

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			1	9		10
missense			38	5		43
nonsense	1	2				3
start loss			1			1
frameshift			1			1
inframe indel						0
splice donor/acceptor (+/-2bp)	1		1			2
splice region			1			1
non coding			3			3
Total	2	2	45	14	0

Highest pathogenic variant AF is 0.00000657

Variants in FAM149B1

This is a list of pathogenic ClinVar variants found in the FAM149B1 region.

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

Position	Type	Phenotype	Significance	ClinVar
10-73168341-T-G		Joubert syndrome 36 • not specified	Uncertain significance (Jul 08, 2024)
10-73174694-A-T		not specified	Uncertain significance (Aug 12, 2021)
10-73177859-A-G		not specified	Uncertain significance (Oct 16, 2023)
10-73177866-A-C		not specified	Uncertain significance (Jul 12, 2023)
10-73177871-T-C		not specified	Likely benign (Apr 05, 2023)
10-73177872-C-G		not specified	Uncertain significance (Jan 10, 2023)
10-73177880-T-G		FAM149B1-related disorder • not specified	Uncertain significance (Apr 22, 2023)
10-73177927-C-T			Uncertain significance (Apr 10, 2023)
10-73192573-C-T			Likely benign (Apr 01, 2022)
10-73192622-G-A		not specified	Uncertain significance (Mar 18, 2024)
10-73192628-AAG-A		Joubert syndrome 36 • Familial aplasia of the vermis	Likely pathogenic (Sep 22, 2024)
10-73192683-G-A		not specified	Uncertain significance (Jan 03, 2024)
10-73192686-T-G		not specified	Uncertain significance (Mar 29, 2022)
10-73193490-C-T		Joubert syndrome 36	Pathogenic (Feb 04, 2020)
10-73193499-A-C		not specified	Uncertain significance (Jul 14, 2024)
10-73193550-G-A		not specified	Uncertain significance (Sep 27, 2022)
10-73193566-C-A		not specified	Uncertain significance (Sep 16, 2021)
10-73193566-C-T		not specified	Uncertain significance (Sep 12, 2023)
10-73193569-T-C		not specified	Uncertain significance (Mar 20, 2023)
10-73208661-T-C			Likely benign (Oct 01, 2023)
10-73208664-TCATAAAG-T			Uncertain significance (Feb 12, 2024)
10-73208678-C-G		not specified	Uncertain significance (May 13, 2024)
10-73208697-C-T			Likely benign (May 01, 2023)
10-73208736-C-A			Likely benign (Dec 01, 2023)
10-73208741-CAGAA-C			Uncertain significance (Feb 07, 2024)

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