SPTBN5

Chr 15

spectrin beta, non-erythrocytic 5

Also known as: BSPECV, HUBSPECV, HUSPECV

NCBI Gene: 51332 ENSG00000137877 UniProt: Q9NRC6 OMIM: 605916

Enables cytoskeletal protein binding activity; dynein intermediate chain binding activity; and identical protein binding activity. Acts upstream of or within Golgi organization and lysosomal transport. Located in cytoplasm; photoreceptor connecting cilium; and photoreceptor disc membrane. [provided by Alliance of Genome Resources, Jul 2025]

OMIM Research

OMIM ResearchGenerating clinical summary…

Active trials

Pubs (1 yr)

—

P/LP submissions

—

P/LP missense

1.06

LOEUF

Multiple*

Mechanism· predicted

Population Genetics & Constraint

gnomAD v4 — loss-of-function & missense intolerance

gnomAD

Tolerant — LoF & missense variants common in population

LoF Constraint?

1.06LOEUF

pLI 0.000

Z-score 0.77

OE 0.94 (0.83–1.06)

Tolerant

Highly tolerant — LoF variants common in population

Missense Constraint?

-1.24Z-score

OE missense 1.08 (1.04–1.12)

2146 obs / 1990.0 exp

Tolerant

Tolerant to missense variation

Observed / Expected Ratios?

LoF OE?0.94 (0.83–1.06)

0≤0.351.4

Missense OE?1.08 (1.04–1.12)

0≤0.61.4

Synonymous OE?1.04

0≤1.21.6

LoF obs/exp: 186 / 197.7Missense obs/exp: 2146 / 1990.0Syn Z: -1.01

Background carrier burden — how many people carry a rare variant somewhere in SPTBN5?

gnomAD v4 · ~731k individuals · PASS only

Rare means allele frequency under

Rare missense

1 in 8

5,413 rare PASS variants

Rare truncating (LoF)

1 in 68

1,024 rare PASS variants

Rare synonymous (reference)

1 in 18

2,284 rare PASS variants

Truncating variants are far rarer here than missense — that gap, in human units, is what constraint means for SPTBN5. A background rate for each class, not the frequency of any particular variant; thin-coverage exons undercount.

By genetic ancestry · 9 gnomAD groups · rare = under 0.1% in that group

Group	People	Missense	Truncating
European (non-Finnish)	~556k	1 in 11	1 in 75
South Asian	~43k	1 in 7	1 in 57
Remaining (unassigned)	~30k	1 in 7	1 in 61
European (Finnish)	~27k	1 in 23	1 in 170
Admixed American	~22k	1 in 8	1 in 61
African / African American	~21k	1 in 7	1 in 71
East Asian	~20k	1 in 9	1 in 99
Ashkenazi Jewish	~13k	1 in 34	1 in 120
Middle Eastern	~2,884	1 in 8	1 in 86

Each group is summed over the variants that are rare in that group. Differences mostly reflect how many people were sampled and how much variation each ancestry carries, not disease risk.

Exome coverage (gnomAD): 63 of 67 coding exons well covered in gnomAD exomes; exons 20, 29, 32, 47 marginal. Genomes: 66 of 67 (exon 20 below).? see exons ↓