Is SRP72 p.Ser282= (c.846C>T) pathogenic?

SRP72 p.Ser282= (c.846C>T) is classified Likely benign in SRP72 (ClinVar, Multiple submitters, 2 submitters; last evaluated 2025-03-28). Absent from gnomAD v4.1.

How common is SRP72 p.Ser282= (c.846C>T) in the general population?

SRP72 p.Ser282= (c.846C>T) is absent from gnomAD v4.1 (gnomAD).

SRP72 p.Ser282=

c.846C>T · rs778556077 · VCV2124696

Likely benign Multiple submitters

Classification

Likely benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 2 submitters

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 -1.5	GERP -2.2
Overall
CADD	6.954	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: SRP72
Protein: p.Ser282=
Coding: c.846C>T
MANE Select: NM_006947
dbSNP: rs778556077
Type: single nucleotide variant
Location: chr4:56483159 (GRCh38)
Gene constraint: LOEUF 0.58 · pLI 0.02 (gnomAD)
Structure: AlphaFold pLDDT 82.76 · 7 PDB
Residue 282: an α-helix

Full SRP72 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

SRP72 c.1502+1G>A Uncertain significance ★★ same type
SRP72 c.1640+4A>G Uncertain significance ★★ same type
SRP72 c.768-9T>G Uncertain significance ★★ same type
SRP72 p.Ala13Thr Uncertain significance ★★ ⚠ same type
SRP72 p.Ala156Gly Uncertain significance ★★ ⚠ same type
SRP72 p.Ala185Val Uncertain significance ★★ ⚠ same type
SRP72 p.Ala291Val Uncertain significance ★★ ⚠ same type
SRP72 p.Ala314Val 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/srp72-p-ser282 (accessed [today's date]).

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