NRAP

nebulin related anchoring protein, the group of LIM domain containing

Basic information

Region (hg38): 10:113588714-113664070

Links

ENSG00000197893 ∙ NCBI:4892 ∙ OMIM:602873 ∙ HGNC:7988 ∙ Uniprot:Q86VF7 ∙ 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 NRAP gene.

• not provided (2 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the NRAP 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				14	14	28
missense			80	17	22	119
nonsense	1		2			3
start loss						0
frameshift	1					1
inframe indel				1		1
splice donor/acceptor (+/-2bp)		3	1	1		5
splice region			1	3	8	12
non coding			19	5	64	88
Total	2	3	102	38	100

Highest pathogenic variant AF is 0.0000131

Variants in NRAP

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

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

Position	Type	Phenotype	Significance	ClinVar
10-113588718-C-T		Factor VII Marburg I Variant Thrombophilia	Uncertain significance (Jan 12, 2018)
10-113588729-A-C		Factor VII Marburg I Variant Thrombophilia	Uncertain significance (Jan 12, 2018)
10-113588734-A-G		Factor VII Marburg I Variant Thrombophilia	Likely benign (Jan 13, 2018)
10-113588787-C-T		Factor VII Marburg I Variant Thrombophilia	Uncertain significance (Jan 13, 2018)
10-113588836-C-T		Factor VII Marburg I Variant Thrombophilia	Uncertain significance (Jan 13, 2018)
10-113588896-C-T		Factor VII Marburg I Variant Thrombophilia	Uncertain significance (Jan 13, 2018)
10-113588934-A-G		Factor VII Marburg I Variant Thrombophilia	Likely benign (Jan 13, 2018)
10-113588967-GA-G		Factor VII Marburg I Variant Thrombophilia	Benign/Likely benign (May 04, 2021)
10-113588989-CCTT-C		Factor VII Marburg I Variant Thrombophilia • NRAP-related disorder	Benign/Likely benign (Dec 31, 2019)
10-113589001-T-C		Inborn genetic diseases	Uncertain significance (Aug 16, 2021)
10-113589013-T-G		Factor VII Marburg I Variant Thrombophilia	Uncertain significance (Jan 13, 2018)
10-113589048-T-A		Inborn genetic diseases	Uncertain significance (Jun 03, 2024)
10-113589051-T-G		Factor VII Marburg I Variant Thrombophilia	Uncertain significance (Jan 13, 2018)
10-113589060-T-A		NRAP-related disorder	Uncertain significance (Sep 13, 2024)
10-113589082-G-A		NRAP-related disorder	Uncertain significance (Jan 17, 2023)
10-113589134-C-T		Factor VII Marburg I Variant Thrombophilia	Uncertain significance (Jan 13, 2018)
10-113589157-G-A		Factor VII Marburg I Variant Thrombophilia	Benign (May 14, 2021)
10-113589171-G-T		Factor VII Marburg I Variant Thrombophilia	Uncertain significance (Jan 12, 2018)
10-113589182-C-T		Factor VII Marburg I Variant Thrombophilia	Uncertain significance (Jan 12, 2018)
10-113589191-C-T		Factor VII Marburg I Variant Thrombophilia	Uncertain significance (Jan 12, 2018)
10-113589192-C-T		Factor VII Marburg I Variant Thrombophilia	Uncertain significance (Jan 13, 2018)
10-113589228-A-G		Factor VII Marburg I Variant Thrombophilia	Uncertain significance (Jan 13, 2018)
10-113589238-T-G		Factor VII Marburg I Variant Thrombophilia	Likely benign (Jan 12, 2018)
10-113589288-T-G		Factor VII Marburg I Variant Thrombophilia	Uncertain significance (Jan 13, 2018)
10-113589408-T-C		Factor VII Marburg I Variant Thrombophilia	Uncertain significance (Jan 13, 2018)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
NRAP	protein_coding	protein_coding	ENST00000359988	42	75412

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
3.26e-50	0.0000421	125099	1	648	125748	0.00258

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.170	999	984	1.02	0.0000549	11477
Missense in Polyphen		371	397.78	0.93267		4807
Synonymous	-0.0417	376	375	1.00	0.0000225	3097
Loss of Function	1.55	86	103	0.835	0.00000567	1201

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0113	0.0112
Ashkenazi Jewish	0.000994	0.000993
East Asian	0.00263	0.00256
Finnish	0.00630	0.00626
European (Non-Finnish)	0.00133	0.00132
Middle Eastern	0.00263	0.00256
South Asian	0.00253	0.00252
Other	0.00296	0.00294

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May be involved in anchoring the terminal actin filaments in the myofibril to the membrane and in transmitting tension from the myofibrils to the extracellular matrix. {ECO:0000250|UniProtKB:Q80XB4}.

Recessive Scores

• pRec: 0.0983

Intolerance Scores

• loftool: 0.984
• rvis_EVS: 3.12
• rvis_percentile_EVS: 99.27

Haploinsufficiency Scores

• pHI: 0.0579
• hipred: Y
• hipred_score: 0.507
• ghis: 0.435

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.326

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Nrap

Gene ontology

• Biological process: biological_process;muscle fiber development;cardiac muscle thin filament assembly
• Cellular component: fascia adherens;muscle tendon junction;Z disc
• Molecular function: actin binding;protein binding;metal ion binding;actin filament binding;muscle alpha-actinin binding