Is SPRED1 p.Val47= (c.141C>T) pathogenic?

SPRED1 p.Val47= (c.141C>T) is classified Likely benign in SPRED1 (ClinVar, Single submitter, 1 submitter; last evaluated 2025-05-24). Very rare (popmax 0.00167%, amr); Associated with Cardiovascular phenotype.

What condition is associated with SPRED1 p.Val47= (c.141C>T)?

SPRED1 p.Val47= (c.141C>T) is associated with Cardiovascular phenotype (ClinVar).

How common is SPRED1 p.Val47= (c.141C>T) in the general population?

SPRED1 p.Val47= (c.141C>T) is very rare (popmax 0.00167%, amr) (gnomAD).

SPRED1 p.Val47=

c.141C>T · VCV3961403

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

very rare (popmax 0.00167%, amr)

Conditions

Cardiovascular phenotype

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 2.7	GERP 2.5, phastCons 1
Overall
CADD	11.28	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.00167% Admixed American · 1/59,992 alleles

Overall 0.000124% 2/1,613,992 alleles · very rare exomes 2/1,461,752 · genomes 0/152,240 · joint denominator

Ancestry group	Frequency	1 in
Admixed Americangrpmax	0.00167%	59,992
European (non-Finnish)	8.47e-05%	1,179,949

Rarity supports pathogenicity (ACMG PM2); frequency above a disease-specific BA1/BS1 threshold argues against it. A variant frequent in one ancestry group can be near-absent in others, so a single global figure can mislead.

Variant & gene context

Gene: SPRED1
Protein: p.Val47=
Coding: c.141C>T
MANE Select: NM_152594
Type: single nucleotide variant
Location: chr15:38299481 (GRCh38)
Gene constraint: LOEUF 0.496 · pLI 0.98 · ClinGen HI 3/3 (gnomAD)
Structure: AlphaFold pLDDT 63.67 · 3 PDB
Residue 47: a β-strand; the wh1 domain

Full SPRED1 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

Cardiovascular phenotype — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Similar variants

SPRED1 p.Arg16Ter Pathogenic ★★ same condition
SPRED1 p.Ala137Val Uncertain significance ★★ ⚠ same condition
SPRED1 p.Ala183Thr Uncertain significance ★★ ⚠ same condition
SPRED1 p.Ala19Gly Uncertain significance ★★ ⚠ same condition
SPRED1 p.Ala406Val Uncertain significance ★★ ⚠ same condition
SPRED1 p.Arg118Lys Uncertain significance ★★ ⚠ same condition
SPRED1 p.Arg16Gln Uncertain significance ★★ same condition
SPRED1 p.Arg214Trp Uncertain significance ★★ ⚠ same condition

Built on 18 open, versioned datasets — ClinVar, gnomAD, AlphaMissense, REVEL, ClinGen & more — plus Sugi Variant's own cross-source analysis. Source data 2026-01–2026-10, ClinVar 2026-10. Full sources & versions →

Cite Sugi Variant

Gür T. Sugi Variant: A Deterministic Per-Variant Germline Reference from a Knowledge Graph for Humans and AI Agents. 2026. doi:10.5281/zenodo.21509445. This variant: https://sugi.bio/variant/spred1-p-val47 (accessed [today's date]).

Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown