FAM161A

FAM161 centrosomal protein A

Basic information

Region (hg38): 2:61824848-61854143

Previous symbols: [ "RP28" ]

Links

ENSG00000170264 ∙ NCBI:84140 ∙ OMIM:613596 ∙ HGNC:25808 ∙ Uniprot:Q3B820 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• retinitis pigmentosa 28 (Strong), mode of inheritance: AR
• retinitis pigmentosa (Supportive), mode of inheritance: AD
• retinitis pigmentosa 28 (Definitive), mode of inheritance: AR

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Retitinis pigmentosa 28	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	Ophthalmologic	10507729; 20705279; 20705278

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the FAM161A gene.

• not provided (85 variants)
• Retinitis pigmentosa 28 (12 variants)
• Retinitis pigmentosa (7 variants)
• Retinal dystrophy (6 variants)
• Autosomal recessive retinitis pigmentosa (3 variants)
• Cone-rod dystrophy (1 variants)
• Inborn genetic diseases (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the FAM161A 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	264	4	271
missense			237	3	4	244
nonsense	33	21	3			57
start loss			1			1
frameshift	54	37	3			94
inframe indel			4			4
splice donor/acceptor (+/-2bp)	1	8				9
splice region			8	24		32
non coding			31	44	10	85
Total	88	66	282	311	18

Highest pathogenic variant AF is 0.000276

Variants in FAM161A

This is a list of pathogenic ClinVar variants found in the FAM161A region.

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

Position	Type	Phenotype	Significance	ClinVar
2-61824904-T-G		Retinitis pigmentosa	Uncertain significance (Jan 13, 2018)
2-61824906-C-A		Retinitis pigmentosa	Uncertain significance (Jan 13, 2018)
2-61824948-C-G		Retinitis pigmentosa	Uncertain significance (Jan 12, 2018)
2-61825023-A-G		Retinitis pigmentosa	Uncertain significance (Jan 13, 2018)
2-61825087-T-G		Retinitis pigmentosa	Uncertain significance (Jan 13, 2018)
2-61825106-T-C		Retinitis pigmentosa	Uncertain significance (Jan 13, 2018)
2-61825110-C-T		Retinitis pigmentosa	Uncertain significance (Jan 13, 2018)
2-61825156-A-G		Retinitis pigmentosa	Uncertain significance (Jan 12, 2018)
2-61825203-T-C		Retinitis pigmentosa	Uncertain significance (Jan 13, 2018)
2-61825232-T-C		Retinitis pigmentosa	Uncertain significance (Jan 12, 2018)
2-61825245-A-G		Retinitis pigmentosa	Benign (Jan 12, 2018)
2-61825311-A-C		Retinitis pigmentosa	Uncertain significance (Jan 13, 2018)
2-61825319-C-A		Retinitis pigmentosa	Uncertain significance (Jan 13, 2018)
2-61825326-T-G		Retinitis pigmentosa	Uncertain significance (Jan 13, 2018)
2-61825355-A-G		Retinitis pigmentosa	Conflicting classifications of pathogenicity (Mar 01, 2023)
2-61825639-CT-C		Retinitis Pigmentosa, Recessive	Uncertain significance (Jun 14, 2016)
2-61825643-T-TC		Retinitis Pigmentosa, Recessive	Uncertain significance (Jun 14, 2016)
2-61825653-T-C		Retinitis pigmentosa	Uncertain significance (Jan 13, 2018)
2-61825660-C-T		Retinitis pigmentosa	Uncertain significance (Jan 12, 2018)
2-61825698-C-T		Retinitis pigmentosa	Uncertain significance (Jan 13, 2018)
2-61825700-C-T		Retinitis pigmentosa	Uncertain significance (Jan 12, 2018)
2-61825703-T-C		Retinitis pigmentosa	Uncertain significance (Jan 12, 2018)
2-61825838-C-T		Retinitis pigmentosa	Uncertain significance (Jan 13, 2018)
2-61825930-C-A		Retinitis pigmentosa	Uncertain significance (Jan 13, 2018)
2-61825932-C-T		Retinitis pigmentosa	Uncertain significance (Jan 13, 2018)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
FAM161A	protein_coding	protein_coding	ENST00000404929	7	29290

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
5.10e-13	0.553	124760	0	34	124794	0.000136

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.495	388	362	1.07	0.0000184	4692
Missense in Polyphen		112	107.91	1.0379		1555
Synonymous	0.0110	133	133	0.999	0.00000673	1295
Loss of Function	1.49	24	33.3	0.721	0.00000212	427

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000575	0.0000556
Finnish	0.000714	0.000696
European (Non-Finnish)	0.000130	0.000124
Middle Eastern	0.0000575	0.0000556
South Asian	0.000135	0.000131
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Involved in ciliogenesis. {ECO:0000269|PubMed:22940612}.

Intolerance Scores

• loftool: 0.851
• rvis_EVS: 1.02
• rvis_percentile_EVS: 91.05

Haploinsufficiency Scores

• hipred: N
• hipred_score: 0.123
• ghis: 0.477

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.795

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Fam161a
• Phenotype: cellular phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); hematopoietic system phenotype; cardiovascular system phenotype (the observable morphological and physiological characteristics of the mammalian heart, blood vessels, or circulatory system that are manifested through development and lifespan); nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan); vision/eye phenotype; immune system phenotype

Gene ontology

• Biological process: visual perception;cilium organization;response to stimulus;cilium assembly;positive regulation of protein acetylation
• Cellular component: astral microtubule;photoreceptor inner segment;centrosome;spindle microtubule;photoreceptor connecting cilium;ciliary basal body;mitotic spindle;mitotic spindle pole
• Molecular function: protein binding;microtubule binding;identical protein binding