FAM161A

protein-coding

FAM161 centrosomal protein A

Gene summary

This gene belongs to the FAM161 family. It is expressed mainly in the retina. Mouse studies suggested that this gene is involved in development of retinal progenitors during embryogenesis, and that its activity is restricted to mature photoreceptors after birth. Mutations in this gene cause autosomal recessive retinitis pigmentosa-28. Alternatively spliced transcript variants have been identified.[provided by RefSeq, Jan 2011]

Previous symbols:

RP28

MANE transcript

NM_001201543.2

Inheritance

AD, AR

ClinVar variants

P:195U:340B:322

Top phenotype

Retitinis pigmentosa 28

gnomAD constraint

pLI —, LoF o/e 0.72

Max pathogenic AF

—

Genomic locus

chr2:61,824,848-61,854,143

External References & Databases

Ensembl (ENSG00000170264)

Transcript & Mutation Effects

hg38 • Region Span ~29.3 kb

Loading mutation effect viewer...

GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

retinitis pigmentosaSUPPORTIVE

Inheritance Pattern: AD

Disease ID:MONDO:0019200

Submitter: Orphanet

retinitis pigmentosa 28STRONG

Inheritance Pattern: AR

Disease ID:MONDO:0011630

Submitter: Labcorp Genetics (formerly Invitae)

retinitis pigmentosa 28STRONG

Inheritance Pattern: AR

Disease ID:MONDO:0011630

Submitter: PanelApp Australia

retinitis pigmentosa 28DEFINITIVE

Inheritance Pattern: AR

Disease ID:MONDO:0011630

Submitter: G2P

retinitis pigmentosa 28DEFINITIVE

Inheritance Pattern: AR

Disease ID:MONDO:0011630

Submitter: Natera

Clinical Genomic Database (CGD)

Retitinis pigmentosa 28AR

Manifestation: Ophthalmologic

Intervention: General

Rationale: 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

Refs: 10507729; 20705279; 20705278

Source: CGD (NHGRI)

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to FAM161A variants in ClinVar

9 Conditions Cataloged

not providedTotal: 772

Retinitis pigmentosa 28Total: 245

Inborn genetic diseasesTotal: 115

FAM161A-related disorderTotal: 85

not specifiedTotal: 77

Retinitis pigmentosaTotal: 66

Retinal dystrophyTotal: 35

Autosomal recessive retinitis pigmentosaTotal: 3

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_001201543.2. 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			14 clinvar	291 clinvar		305
missense	1 clinvar	2 clinvar	316 clinvar	28 clinvar	3 clinvar	350
nonsense	29 clinvar	37 clinvar	4 clinvar			70
start loss			1 clinvar			1
frameshift	53 clinvar	60 clinvar	4 clinvar			117
splice donor/acceptor (+/-2bp)	2 clinvar	11 clinvar	1 clinvar			14
Total	85	110	340	319	3	857

Highest pathogenic variant AF is 0.00041568733

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 16 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_001201543.2	RefSeq	NP_001188472.1	7	MANE Select
ENST00000404929.6	Ensembl	ENSP00000385158.1	7	MANE Select
NM_032180.3	RefSeq	NP_115556.2	6	Standard
ENST00000307507.3	Ensembl	ENSP00000303170.3	2	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

visual perception
cilium organization
response to stimulus
cilium assembly
positive regulation of protein acetylation

Molecular Function

protein binding
microtubule binding
identical protein binding

Cellular Component

astral microtubule
photoreceptor inner segment
centrosome
spindle microtubule
photoreceptor connecting cilium

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000404929
Coding exons: 7
Length: 29290
Individuals with no LoFs: 124760
Homozygous LoFs: 0
Heterozygous LoFs: 34
Defined: 124794
p: 0.000136

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	-0.495	388	362	1.07	0.0000184	4692
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0	0.0	absent
Latino/Admixed American	0	0.0	absent
Ashkenazi Jewish	0	0.0	absent
East Asian	0.000057	0.000056	rare
Finnish	0.00071	0.00070	rare
European (Non-Finnish)	0.00013	0.00012	rare
South Asian	0.00014	0.00013	rare
Other	0	0.0	absent

dbNSFP Gene Annotations

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

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: E
Indispensability score: 0.795

Gene Damage Prediction

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