Is SELP p.Arg429= (c.1285C>A) pathogenic?

SELP p.Arg429= (c.1285C>A) is classified Likely benign in SELP (ClinVar, Single submitter, 1 submitter; last evaluated 2024-07-01). Very rare (popmax 0.00167%, amr).

How common is SELP p.Arg429= (c.1285C>A) in the general population?

SELP p.Arg429= (c.1285C>A) is very rare (popmax 0.00167%, amr) (gnomAD).

SELP p.Arg429=

c.1285C>A · rs761957913 · VCV3250705

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

very rare (popmax 0.00167%, amr)

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
Pangolin	Δ0.31	loss · gain 0.01 · not in the SpliceAI release · independent
Constraint at this position
Conservation	phyloP 1.1	GERP 0.09
Overall
CADD	4.673	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.00167% Admixed American · 1/60,004 alleles

Filtering AF 0.000247% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.000159%

Overall 0.000496% 8/1,613,986 alleles · very rare exomes 8/1,461,776 · genomes 0/152,210 · joint denominator

Ancestry group	Frequency	1 in
Admixed Americangrpmax	0.00167%	60,004
European (non-Finnish)	0.000593%	168,565

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: SELP
Protein: p.Arg429=
Coding: c.1285C>A
MANE Select: NM_003005
dbSNP: rs761957913
Type: single nucleotide variant
Location: chr1:169609552 (GRCh38)
Gene constraint: LOEUF 0.972 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 80.27 · 5 PDB
Residue 429: the sushi 4 domain

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

Similar variants

SELP p.Arg429Leu Uncertain significance ★ ⚠ same residue
SELP p.Asn128= Benign ★★ same type
SELP p.Asn673Ser Benign ★★ same type
SELP p.Ser619Ala Benign ★★ same type
SELP p.Thr274Ile Benign ★★ same type
SELP p.Thr767= Benign ★★ same type
SELP p.Ala246Val Uncertain significance ★ ⚠ same type
SELP p.Ala329Thr 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/selp-p-arg429 (accessed [today's date]).

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