SPAG7

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				1 clinvar	1 clinvar	2
missense			25 clinvar		1 clinvar	26
nonsense						0
start loss						0
frameshift			1 clinvar			1
splice donor/acceptor (+/-2bp)			4 clinvar			4
Total	0	0	30	1	2	33

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 26 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_004890.3	RefSeq	NP_004881.2	7	MANE Select
ENST00000206020.8	Ensembl	ENSP00000206020.3	7	MANE Select
ENST00000573366.5	Ensembl	ENSP00000458405.1	5	Standard
ENST00000573366.6	Ensembl	ENSP00000458405.1	5	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Molecular Function

nucleic acid binding

Cellular Component

nucleus

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000206020
Coding exons: 7
Length: 8647
Individuals with no LoFs: 124805
Homozygous LoFs: 0
Heterozygous LoFs: 9
Defined: 124814
p: 0.0000361

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.876	107	136	0.788	0.00000801	1500
Missense (PolyPhen)		26	36.116	0.71991		428
Synonymous	-1.77	66	50.1	1.32	0.00000288	408
Loss of Function	1.57	7	13.1	0.532	5.67e-7	158

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	0.0	absent
Finnish	0.000093	0.000046	rare
European (Non-Finnish)	0.000053	0.000053	rare
South Asian	0.000065	0.000065	rare
Other	0	0.0	absent

dbNSFP Gene Annotations

Source: dbNSFP

Recessive Scores

pRec: 0.140

Intolerance Scores

LoFtool: 0.422
RVIS EVS: 0.24
RVIS percentile EVS: 68.98

Essentials

Essential (CRISPR): E
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: E
Indispensability score: 0.975

Gene Damage Prediction

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