ARHGAP19-SLIT1

ARHGAP19-SLIT1 readthrough (NMD candidate)

Basic information

Region (hg38): 10:97153045-97292637

Links

ENSG00000269891 ∙ NCBI:100533184 ∙ ∙ HGNC:48348 ∙ ∙ ∙ 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 ARHGAP19-SLIT1 gene.

• Inborn genetic diseases (27 variants)
• not provided (2 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ARHGAP19-SLIT1 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						0
missense						0
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding			27	2		29
Total	0	0	27	2	0

Variants in ARHGAP19-SLIT1

This is a list of pathogenic ClinVar variants found in the ARHGAP19-SLIT1 region.

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

Position	Type	Phenotype	Significance	ClinVar
10-97163387-C-G		not specified	Uncertain significance (Jan 27, 2022)
10-97163395-T-C		not specified	Uncertain significance (Aug 12, 2021)
10-97164836-G-T			Likely benign (Mar 01, 2023)
10-97164864-C-T		not specified	Uncertain significance (May 14, 2024)
10-97164877-T-A		not specified	Uncertain significance (Jan 03, 2022)
10-97185544-G-T		not specified	Uncertain significance (Mar 22, 2023)
10-97185599-C-G		not specified	Uncertain significance (Jan 31, 2023)
10-97185632-G-A		not specified	Uncertain significance (Aug 02, 2021)
10-97185649-G-A		not specified	Uncertain significance (Nov 17, 2022)
10-97229200-G-A		not specified	Uncertain significance (May 03, 2023)
10-97229783-C-T		not specified	Uncertain significance (Jul 27, 2024)
10-97229804-A-G		not specified	Uncertain significance (Nov 13, 2024)
10-97235249-C-T		not specified	Uncertain significance (Jan 23, 2023)
10-97235255-T-C		not specified	Uncertain significance (Apr 01, 2024)
10-97235281-C-A		not specified	Uncertain significance (Dec 01, 2022)
10-97235285-C-T		not specified	Uncertain significance (Aug 20, 2024)
10-97235306-G-C		not specified	Uncertain significance (May 20, 2024)
10-97243975-A-G		not specified	Uncertain significance (Nov 21, 2022)
10-97244015-C-T		not specified	Uncertain significance (Aug 21, 2023)
10-97244047-G-A		not specified	Uncertain significance (Dec 09, 2023)
10-97244060-T-C		not specified	Uncertain significance (Aug 16, 2022)
10-97244090-G-A		not specified	Uncertain significance (May 14, 2024)
10-97244120-A-G		not specified	Uncertain significance (Dec 04, 2024)
10-97246280-C-A		not specified	Uncertain significance (Feb 17, 2022)
10-97246304-G-A			Likely benign (Apr 01, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ARHGAP19-SLIT1	protein_coding	protein_coding	ENST00000453547	13	294619

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
6.98e-12	0.638	125644	1	103	125748	0.000414

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.334	272	288	0.945	0.0000155	3389
Missense in Polyphen		73	89.519	0.81547		1065
Synonymous	1.33	89	107	0.836	0.00000567	990
Loss of Function	1.51	22	31.1	0.708	0.00000181	352

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000598	0.000597
Ashkenazi Jewish	0.0000992	0.0000992
East Asian	0.000707	0.000707
Finnish	0.000185	0.000185
European (Non-Finnish)	0.000388	0.000387
Middle Eastern	0.000707	0.000707
South Asian	0.000916	0.000882
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Haploinsufficiency Scores

• hipred: N
• hipred_score: 0.163

Gene Damage Prediction

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