Is SPIN4 p.Ala143= (c.429G>A) pathogenic?

SPIN4 p.Ala143= (c.429G>A) is classified Likely benign in SPIN4 (ClinVar, Single submitter, 1 submitter; last evaluated 2026-06-01). Absent from gnomAD v4.1.

How common is SPIN4 p.Ala143= (c.429G>A) in the general population?

SPIN4 p.Ala143= (c.429G>A) is absent from gnomAD v4.1 (gnomAD).

SPIN4 p.Ala143=

c.429G>A · VCV4873649

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Absent

absent from gnomAD v4.1

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 -7.7	GERP -3.4
Overall
CADD	8.3	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Absent from gnomAD v4.1. Not observed in any sequenced alleles — a rarity signal (ACMG PM2-supporting), not evidence of pathogenicity on its own.

Variant & gene context

Gene: SPIN4
Protein: p.Ala143=
Coding: c.429G>A
MANE Select: NM_001012968
Type: single nucleotide variant
Location: chrX:63350391 (GRCh38)
Structure: AlphaFold pLDDT 82.17 · 2 PDB
Residue 143: a β-strand; the 'tudor-like domain 2' region

Full SPIN4 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

SPIN4 p.Arg144Leu Uncertain significance ★ ⚠ same type
SPIN4 p.Arg37Gly Uncertain significance ★ ⚠ same type
SPIN4 p.Arg38Lys Uncertain significance ★ ⚠ same type
SPIN4 p.His207Gln Uncertain significance ★ ⚠ same type
SPIN4 p.Met148Ile Uncertain significance ★ ⚠ same type
SPIN4 p.Ser117Cys Uncertain significance ★ ⚠ same type
SPIN4 p.Ser2Tyr Uncertain significance ★ ⚠ same type
SPIN4 p.Tyr163Ser Uncertain significance ★ ⚠ same type

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/spin4-p-ala143 (accessed [today's date]).

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