Is RELB p.Ser425Phe (c.1274C>T) pathogenic?

RELB p.Ser425Phe (c.1274C>T) is classified Uncertain significance in RELB (ClinVar, Multiple submitters, 2 submitters; last evaluated 2025-08-20). AlphaMissense: ambiguous (0.4506); Ultra-rare (popmax 0.012%, afr).

How common is RELB p.Ser425Phe (c.1274C>T) in the general population?

RELB p.Ser425Phe (c.1274C>T) is ultra-rare (popmax 0.012%, afr) (gnomAD).

What do computational predictors say about RELB p.Ser425Phe (c.1274C>T)?

AlphaMissense predicts ambiguous (score 0.4506) — an in-silico prediction, not a clinical call.

RELB p.Ser425Phe

c.1274C>T · rs367810360 · VCV2420868

Uncertain significance Multiple submitters

Classification

Uncertain significance

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 2 submitters

AlphaMissense

ambiguous

0.4506 · ACMG-weighted

gnomAD v4.1

Rare

ultra-rare (popmax 0.012%, afr)

Missense predictors

0/2 damaging

REVEL, SaProt · AlphaMissense indeterminate

Computational evidence

Protein change
AlphaMissense	0.4506	ambiguous
REVEL	0.141	moderately benign-leaning
SaProt	LLR -5.67	tolerated
⇒ REVEL and SaProt both call this tolerated; AlphaMissense is indeterminate.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 7.6	GERP 1.8, phastCons 1
Regional constraint	o/e 0.78	unconstrained · MANE · 12 kb · p 4.5e-06 · regional, not allelic
Overall
CADD	33.0	PHRED · no single calibrated threshold — expert panels disagree

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

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.012% African / African-American · 9/74,922 alleles

Filtering AF 0.00623% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.00468%

Overall 0.000868% 14/1,613,652 alleles · ultra-rare exomes 6/1,461,474 · genomes 8/152,178 · joint denominator

Ancestry group	Frequency	1 in
African / African-Americangrpmax	0.012%	8,325
Admixed American	0.00834%	11,997

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: RELB
Protein: p.Ser425Phe
Coding: c.1274C>T
MANE Select: NM_006509
dbSNP: rs367810360
Type: single nucleotide variant
Location: chr19:45034310 (GRCh38)
Gene constraint: LOEUF 0.512 · pLI 0.97 (gnomAD)
Structure: AlphaFold pLDDT 70.42 · 1 PDB
Residue 425: the rhd domain; a UniProt-annotated variant site (in imd53)

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

Similar variants

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RELB p.Ala565Val Uncertain significance ★★ ⚠ same type
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RELB p.Arg211Gln Uncertain significance ★★ ⚠ same type
RELB p.Arg213Gln Uncertain significance ★★ ⚠ same type
RELB p.Arg213Trp Uncertain significance ★★ ⚠ same type
RELB p.Arg219Gln Uncertain significance ★★ ⚠ same type
RELB p.Arg241Trp 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/relb-p-ser425phe (accessed [today's date]).

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