Is SGCA p.Phe6Val (c.16T>G) pathogenic?

SGCA p.Phe6Val (c.16T>G) is classified Uncertain significance in SGCA (ClinVar, Single submitter, 1 submitter; last evaluated 2025-08-01). AlphaMissense: likely benign (0.0652); Absent from gnomAD v4.1; Associated with Inborn genetic diseases.

What condition is associated with SGCA p.Phe6Val (c.16T>G)?

SGCA p.Phe6Val (c.16T>G) is associated with Inborn genetic diseases (ClinVar).

How common is SGCA p.Phe6Val (c.16T>G) in the general population?

SGCA p.Phe6Val (c.16T>G) is absent from gnomAD v4.1 (gnomAD).

What do computational predictors say about SGCA p.Phe6Val (c.16T>G)?

AlphaMissense predicts likely benign (score 0.0652) — an in-silico prediction, not a clinical call.

SGCA p.Phe6Val

c.16T>G · VCV4163689

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.0652 · ACMG-weighted

gnomAD v4.1

Absent

absent from gnomAD v4.1

Missense predictors

0/3 damaging

AlphaMissense, REVEL, SaProt

Conditions

Inborn genetic diseases

Computational evidence

Protein change
AlphaMissense	0.0652	likely benign
REVEL	0.147	moderately benign-leaning
SaProt	LLR -4.91	tolerated
⇒ AlphaMissense, REVEL and SaProt all call this tolerated.
Splicing
SpliceAI	<0.2	no splice effect predicted · four deltas, not one · how we know
Constraint at this position
Conservation	phyloP -0.73	GERP -2
Regional constraint	o/e 0.91	unconstrained · MANE · 9,393 bp · p 0.033 · regional, not allelic
Overall
CADD	0.015	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

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: SGCA
Protein: p.Phe6Val
Coding: c.16T>G
MANE Select: NM_000023
Type: single nucleotide variant
Location: chr17:50166056 (GRCh38)
Gene constraint: LOEUF 1.273 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 80.15

Full SGCA 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

SGCA p.Phe6= Likely benign ★ same residue
SGCA p.Ala220Thr Uncertain significance ★★ ⚠ same condition
SGCA p.Ala290Val Uncertain significance ★★ ⚠ same condition
SGCA p.Arg141His Uncertain significance ★★ ⚠ same condition
SGCA p.Arg156Cys Uncertain significance ★★ ⚠ same condition
SGCA p.Arg156Ser Uncertain significance ★★ ⚠ same condition
SGCA p.Arg184Cys Uncertain significance ★★ ⚠ same condition
SGCA p.Arg192Gln 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/sgca-p-phe6val (accessed [today's date]).

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