NIN p.Asp1312=
c.3936T>C · rs766903270 · VCV744303
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0217%, 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 |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP -0.041 | GERP 0.69 |
| Overall | ||
| CADD | 2.218 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0217%
Admixed American · 13/59,786 alleles
Filtering AF
0.0128%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0102%
Overall
0.00205%
33/1,613,098 alleles · ultra-rare
exomes 26/1,461,022 · genomes 7/152,076 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Admixed Americangrpmax | 0.0217% | 4,599 |
| Middle Eastern | 0.0164% | 6,080 |
| Remaining individualsnot grpmax-eligible | 0.0048% | 20,815 |
| South Asian | 0.0022% | 45,480 |
| African / African-American | 0.00134% | 74,778 |
| European (non-Finnish) | 0.0011% | 90,749 |
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
- NIN
- Protein
- p.Asp1312=
- Coding
- c.3936T>C
- MANE Select
- NM_020921
- dbSNP
- rs766903270
- Type
- single nucleotide variant
- Location
- chr14:50757094 (GRCh38)
- Gene constraint
- LOEUF 0.62 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 64.47
- Residue 1312
- the 'important for interaction with cep170' region; the 'interacts with dsp' region
Similar variants
- NIN p.Asp1312Asn Uncertain significance ★ ⚠ same residue
- NIN p.Arg2039Ter Likely pathogenic ★★ same type
- NIN p.Ala1049Thr Uncertain significance ★★ ⚠ same type
- NIN p.Ala1212Val Uncertain significance ★★ ⚠ same type
- NIN p.Ala1350Gly Uncertain significance ★★ ⚠ same type
- NIN p.Ala1741Val Uncertain significance ★★ ⚠ same type
- NIN p.Ala1755Thr Uncertain significance ★★ ⚠ same type
- NIN p.Ala1755Val 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/nin-p-asp1312 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown