Is DECR1 p.Val7Phe (c.19G>T) pathogenic?

DECR1 p.Val7Phe (c.19G>T) is classified Uncertain significance in DECR1 (ClinVar, Single submitter, 1 submitter; last evaluated 2024-03-04). AlphaMissense: likely benign (0.0688); Ultra-rare (popmax 0.0107%, afr).

How common is DECR1 p.Val7Phe (c.19G>T) in the general population?

DECR1 p.Val7Phe (c.19G>T) is ultra-rare (popmax 0.0107%, afr) (gnomAD).

What do computational predictors say about DECR1 p.Val7Phe (c.19G>T)?

AlphaMissense predicts likely benign (score 0.0688) — an in-silico prediction, not a clinical call.

DECR1 p.Val7Phe

c.19G>T · rs1009593027 · VCV3081234

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.0688 · ACMG-weighted

gnomAD v4.1

Rare

ultra-rare (popmax 0.0107%, afr)

Missense predictors

0/3 damaging

AlphaMissense, REVEL, SaProt

Computational evidence

Protein change
AlphaMissense	0.0688	likely benign
REVEL	0.25	benign-leaning
SaProt	LLR -6.89	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 -0.28	GERP -3.2
Regional constraint	o/e 1.06	unconstrained · MANE · 50 kb · p 0.26 · regional, not allelic
Overall
CADD	15.26	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 0.0107% African / African-American · 8/74,942 alleles

Filtering AF 0.00528% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.0038%

Overall 0.000496% 8/1,613,926 alleles · ultra-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: DECR1
Protein: p.Val7Phe
Coding: c.19G>T
MANE Select: NM_001359
dbSNP: rs1009593027
Type: single nucleotide variant
Location: chr8:90001511 (GRCh38)
Gene constraint: LOEUF 1.566 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 89.20 · 3 PDB

Full DECR1 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

DECR1 p.Ala20Thr Uncertain significance ★★ ⚠ same type
DECR1 p.Val207Leu Uncertain significance ★★ ⚠ same type
DECR1 p.Ser26Asn Likely benign ★★ ⚠ same type
DECR1 p.Ala173Val Uncertain significance ★ ⚠ same type
DECR1 p.Ala225Glu Uncertain significance ★ ⚠ same type
DECR1 p.Ala278Thr Uncertain significance ★ ⚠ same type
DECR1 p.Arg251Cys Uncertain significance ★ ⚠ same type
DECR1 p.Arg251His 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/decr1-p-val7phe (accessed [today's date]).

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