RFLNA

refilin A

Basic information

Region (hg38): 12:123973241-124316024

Previous symbols: [ "FAM101A" ]

Links

ENSG00000178882 ∙ NCBI:144347 ∙ OMIM:615927 ∙ HGNC:27051 ∙ Uniprot:Q6ZTI6 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

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

Variants pathogenicity by type

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

Variants in RFLNA

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

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

Position	Type	Phenotype	Significance	ClinVar
12-124012355-A-G		not specified	Uncertain significance (Nov 21, 2022)
12-124012361-A-C		not specified	Uncertain significance (Feb 27, 2024)
12-124012681-G-A			Likely benign (Apr 01, 2023)
12-124012885-A-C		not specified	Uncertain significance (Dec 06, 2022)
12-124012925-A-T		not specified	Uncertain significance (Sep 16, 2021)
12-124314270-G-A			Likely benign (Feb 01, 2023)
12-124314355-GC-G			Uncertain significance (Dec 20, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
RFLNA	protein_coding	protein_coding	ENST00000324038	2	342783

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.233	0.655	125537	0	3	125540	0.0000119

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.390	86	96.8	0.888	0.00000745	870
Missense in Polyphen		29	39.966	0.72562		380
Synonymous	-0.146	42	40.8	1.03	0.00000296	283
Loss of Function	1.14	1	3.19	0.313	1.36e-7	38

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.000111	0.0000993
East Asian	0.0000547	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.00	0.00
Middle Eastern	0.0000547	0.0000544
South Asian	0.0000379	0.0000327
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Involved in the regulation of the perinuclear actin network and nuclear shape through interaction with filamins. Plays an essential role in actin cytoskeleton formation in developing cartilaginous cells. {ECO:0000250|UniProtKB:Q7TS73}.

Recessive Scores

• pRec: 0.111

Intolerance Scores

• rvis_EVS: 0.68
• rvis_percentile_EVS: 84.93

Haploinsufficiency Scores

• pHI: 0.186
• hipred: N
• hipred_score: 0.398
• ghis: 0.425

Essentials

• essential_gene_gene_trap: N

Mouse Genome Informatics

• Gene name: Rflna
• Phenotype: growth/size/body region phenotype; cellular phenotype; normal phenotype; limbs/digits/tail phenotype; skeleton phenotype

Gene ontology

• Biological process: skeletal system morphogenesis;negative regulation of chondrocyte development;actin filament bundle organization;negative regulation of bone mineralization involved in bone maturation
• Cellular component: cytoplasm;actin filament bundle
• Molecular function: protein binding;filamin binding