Is SRP72 p.Ala2= (c.6G>A) pathogenic?

SRP72 p.Ala2= (c.6G>A) is classified Likely benign in SRP72 (ClinVar, Single submitter, 1 submitter; last evaluated 2026-01-10). Very rare (popmax 0.00026%, nfe).

How common is SRP72 p.Ala2= (c.6G>A) in the general population?

SRP72 p.Ala2= (c.6G>A) is very rare (popmax 0.00026%, nfe) (gnomAD).

SRP72 p.Ala2=

c.6G>A · VCV4841459

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

very rare (popmax 0.00026%, nfe)

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 12	GERP 1.9, phastCons 1
Overall
CADD	15.51	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.00026% European (non-Finnish) · 3/1,154,108 alleles

Filtering AF 6.9e-05% ClinGen BA1/BS1 input FAF95, joint · FAF99 1.9e-05%

Overall 0.000192% 3/1,558,996 alleles · very rare exomes 2/1,406,856 · genomes 1/152,140 · joint denominator

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: SRP72
Protein: p.Ala2=
Coding: c.6G>A
MANE Select: NM_006947
Type: single nucleotide variant
Location: chr4:56467641 (GRCh38)
Gene constraint: LOEUF 0.58 · pLI 0.02 (gnomAD)
Structure: AlphaFold pLDDT 82.76 · 7 PDB
Residue 2: a modified residue (n-acetylalanine)

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-ala2 (accessed [today's date]).

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