PDSS2 p.Lys271=
c.813G>A · rs746982042 · VCV2175894
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00517%, 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 0.83 | GERP 0.069, phastCons 1 |
| Overall | ||
| CADD | 8.517 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00517%
European (non-Finnish) · 61/1,179,990 alleles
Filtering AF
0.0041%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00372%
Overall
0.0039%
63/1,614,026 alleles · very rare
exomes 59/1,461,788 · genomes 4/152,238 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| European (non-Finnish)grpmax | 0.00517% | 19,344 |
| Admixed American | 0.00333% | 30,000 |
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
- PDSS2
- Protein
- p.Lys271=
- Coding
- c.813G>A
- MANE Select
- NM_020381
- dbSNP
- rs746982042
- Type
- single nucleotide variant
- Location
- chr6:107212172 (GRCh38)
- Gene constraint
- LOEUF 0.818 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
- Structure
- AlphaFold pLDDT 80.28
Similar variants
- PDSS2 p.Arg163His Uncertain significance ★★ ⚠ same type
- PDSS2 p.Arg366Cys Uncertain significance ★★ ⚠ same type
- PDSS2 p.Arg366His Uncertain significance ★★ ⚠ same type
- PDSS2 p.Arg385Thr Uncertain significance ★★ ⚠ same type
- PDSS2 p.Asn167Ser Uncertain significance ★★ ⚠ same type
- PDSS2 p.Asn201Ser Uncertain significance ★★ ⚠ same type
- PDSS2 p.Asn314Thr Uncertain significance ★★ ⚠ same type
- PDSS2 p.Asn390Ser 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/pdss2-p-lys271 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown