Is SEC24D p.Val90Ile (c.268G>A) pathogenic?

SEC24D p.Val90Ile (c.268G>A) is classified Uncertain significance in SEC24D (ClinVar, Single submitter, 1 submitter; last evaluated 2024-09-04). AlphaMissense: likely benign (0.0723); Very rare (popmax 0.00134%, afr); Associated with Inborn genetic diseases.

What condition is associated with SEC24D p.Val90Ile (c.268G>A)?

SEC24D p.Val90Ile (c.268G>A) is associated with Inborn genetic diseases (ClinVar).

How common is SEC24D p.Val90Ile (c.268G>A) in the general population?

SEC24D p.Val90Ile (c.268G>A) is very rare (popmax 0.00134%, afr) (gnomAD).

What do computational predictors say about SEC24D p.Val90Ile (c.268G>A)?

AlphaMissense predicts likely benign (score 0.0723) — an in-silico prediction, not a clinical call.

SEC24D p.Val90Ile

c.268G>A · VCV3439188

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.0723 · ACMG-weighted

gnomAD v4.1

Rare

very rare (popmax 0.00134%, afr)

Missense predictors

0/3 damaging

AlphaMissense, REVEL, SaProt

Conditions

Inborn genetic diseases

Computational evidence

Protein change
AlphaMissense	0.0723	likely benign
REVEL	0.034	moderately benign-leaning
SaProt	LLR -6.84	tolerated
⇒ AlphaMissense, REVEL and SaProt all call this tolerated.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 0.1	GERP -0.098
Regional constraint	o/e 0.89	unconstrained · MANE · 110 kb · p 0.00018 · regional, not allelic
Overall
CADD	14.15	PHRED · no single calibrated threshold — expert panels disagree

ClinVar classifies this uncertain; the computational predictors unanimously lean tolerated — a triage signal, not a reclassification

AlphaMissense carries the ACMG weight for missense; REVEL and SaProt are independent agreement signals.

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.00134% African / African-American · 1/74,612 alleles

Overall 0.000657% 1/152,120 alleles · very rare

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: SEC24D
Protein: p.Val90Ile
Coding: c.268G>A
MANE Select: NM_014822
Type: single nucleotide variant
Location: chr4:118817393 (GRCh38)
Gene constraint: LOEUF 0.766 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 83.21 · 6 PDB
Residue 90: the 'disordered' region

Full SEC24D gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

Inborn genetic diseases — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Similar variants

SEC24D c.1824+1G>T Likely pathogenic ★★ same condition
SEC24D p.Val90fs Pathogenic/Likely pathogenic ★★ same residue
SEC24D p.Ala218Val Uncertain significance ★★ ⚠ same condition
SEC24D p.Ala570Val Uncertain significance ★★ ⚠ same condition
SEC24D p.Ala774Asp Uncertain significance ★★ ⚠ same condition
SEC24D p.Ala94Thr Uncertain significance ★★ ⚠ same condition
SEC24D p.Arg365Thr Uncertain significance ★★ ⚠ same condition
SEC24D p.Asp1018Asn 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/sec24d-p-val90ile (accessed [today's date]).

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